[BUG] manual curation import binning to profile.db not working

[emily-ap]

Short description of the problem

We are trying to follow this protocol: https://github.com/koszullab/metaTOR/blob/master/docs/example/manual_curation_of_metator_MAGs.md, and the "Import binning" step is not working due to the PROFILE.db missing a table.

anvi'o version

Anvi’o .......................................: marie (v8)
Python .......................................: 3.10.15

anvi-self-test --version

System info

Current OS
Description: Ubuntu 22.04.5 LTS
Release: 22.04
Codename: jammy

Used conda to install anvi'o

conda create -y --name anvio-8 python=3.10

Detailed description of the issue

Using the following tutorial: https://github.com/koszullab/metaTOR/blob/master/docs/example/manual_curation_of_metator_MAGs.md we are trying to manually curate a single bin. When running the "import binning" step, we receive the output attached (see photo and text below):

Config Error: The database at profile/PROFILE.db does not seem to have a table named
mean_coverage_Q2Q3_splits :/ Here is a list of table names this database
knows: self, item_additional_data, item_orders, layer_additional_data,
layer_orders, variable_nucleotides, variable_codons, indels, views,
collections_info, collections_bins_info, collections_of_contigs,
collections_of_splits, states

Files / commands to reproduce the issue

command to reproduce:

anvi-import-collection -c ME2015-04-11_3300034167_anvio.db -p profile/PROFILE.db -C ME201504 --contigs-mode ME2015-04-11_3300034167_binning.tsv

Files are very large but can be uploaded if necessary!

[meren]

That profile-db seems to be broken :/

Can you please send the following output as well:

anvi-db-info profile/PROFILE.db

[emily-ap]

Please see screenshot of output!

[meren]

I will also need this output please:

anvi-export-table profile/PROFILE.db --list

For instance when I run this on a proper database, this is the output I get:

self
item_additional_data
item_orders
layer_additional_data
layer_orders
variable_nucleotides
variable_codons
indels
views
collections_info
collections_bins_info
collections_of_contigs
collections_of_splits
states
protein_abundances
metabolite_abundances
std_coverage_splits
std_coverage_contigs
mean_coverage_splits
mean_coverage_contigs
mean_coverage_Q2Q3_splits
mean_coverage_Q2Q3_contigs
detection_splits
detection_contigs
abundance_splits
abundance_contigs
variability_splits
variability_contigs

If you have a list that differs from this, it is a certainty that the run that generated your profile-db failed at some point, and what you have a the moment is a broken, unfinished output :/

[emily-ap]

See photo:

Yes it looks like ours failed. We can try redoing our earlier steps. Would it matter that we're performing this on a single bin at and therefore are skipping the merging step outlined in the protocol from metaTOR documentation?

protocol referenced: https://github.com/koszullab/metaTOR/blob/master/docs/example/manual_curation_of_metator_MAGs.md

[meren]

That part doesn't matter :)