Closed ziphra closed 4 years ago
@ziphra, I am sorry that you have been having troubles. I reproduced your error and it was due to a bug in which we did not update the list of tables in the database after creating those tables.
I fixed the bug and was able to run anvi-self-test --suite pangenomics
without getting that error anymore. If you do a git pull
to update your anvi'o master your commands should work now, but please let us know if you run into any more issues. :)
It works perfectly! Thank you very much for the quick reply :)
Hi,
I'm having trouble while running the pangenomic workflow.
this command
anvi-gen-genomes-storage -e external-genomes.txt -i internal-genomes.txt -o electrogenes-GENOMES.db
gives meConfig Error: The database at electrogenes-GENOMES.db does seem to have a table `genome_info` :/ Here is a list of table names this database knows:
(and no list printed after), even thought it seemed to work ok since all of my genomes were proceed during the program.Then, after trying
anvi-pan-genome -g electrogenes-GENOMES.db -n electrogenes_pang
I get:
Config Error: Query on genome_info with the where clause of 'genome_name IN ()' did not return anything.
I may have to tell that I updated my contigs database (that I made with Anvi’o) using the --just-do-it flag (I am so ashamed......) because I had sqlite3 version 28 instead of version 30 required at that moment.... And I believe sqlite3 has to do with making databases, now... I since updated to sqlite3 version 31.
But still, the pangenomic self test gives me the same error:
Here, my
anvi-self-test --version
:I am running macOS Catalina version 10.15.4.
In advance, thanks for any help.
Euphrasie