A. Murat Eren (Meren)

It seems one of the gene clusters anvi'o is trying to get alignments for from muscle, is exploding muscle :/ This is an issue anvi'o can do very little. I...

PyFamsa looks very promising and I feel like perhaps anvi'o should completely switch to that and use famsa via a native Python interface, and dump muscle and all the command...

Hi Anna, Yes, there is none for FASTA. I hadn't realized this until you brought it up. Should I do something about it when I can?

Hi @YongyiPeng, Can you please send the output for these two commands after running them in your anvi'o environment? ``` ls `python -c 'import anvio; import os; print(os.path.dirname(anvio.__file__))'`/data/interactive/lib/ ``` ```...

Can you please run this command and send the output: ``` ls `python -c 'import anvio; import os; print(os.path.dirname(anvio.__file__))'`/tests ```

Good. Can you please run these two commands: ``` bash # change directory cd `python -c 'import anvio; import os; print(os.path.dirname(anvio.__file__))'`/tests # run test ./run_component_tests_for_SCVs_SAAVs_structure.sh new ``` At the end...

Good. Please address this problem by following the instructions on the message until you don't see it anymore when you run `./run_component_tests_for_SCVs_SAAVs_structure.sh new` in this directory.

This looks like a memory issue, so there is not much we can do. BUT, there is always a way. In this case, I one could split their contigs-db file...

Yes, unfortunately. That's why it is listed as a Python 2.7 program: https://github.com/meren/illumina-utils/blob/master/setup.py#L33 Someone will have to upgrade to codebase a tiny bit so it is Py3 compatible. It will...

OMG. I was working on this literally just now (with embarrassment associated with not implementing this all this time), and SAW YOUR PR WHICH IS CRAY 😂 Looking at your...