TypeError when running anvi-compute-functional-enrichment on kegg-modules (anvio v7)

[Herdís]

Hello,  

I'm running Anvi'o (v7) through conda (4.10.1) on a HPC Ubuntu (18.04). 

I am following the pangenomics workflow on a set of metagenomes and decided to try the new metabolic reconstruction tools introduced in v7, but am encountering a TypeError I don't know where originates from. Here are the steps leading up to the error:

(1) I ran anvi-estimate-metabolism on the contigs databases and got as output modules.txt in what seems to me proper format (attached as modules)

(2) I created the groups.txt file with the "sample" names corresponding with the entries in the "db_name" column in modules.txt (attached as groups)

(3) and then tried running 

anvi-compute-functional-enrichment -M modules.txt -G groups.txt

and got a TypeError of somewhere a str and int being compared (attached as error)

I am pretty new to all of this, so if the provided info is insufficient let me know!

Any help would be greatly appreciated!

Herdís Steinsdóttir

[Iva Veseli]

Hi Herdís,

It looks like you did everything right, so this must be a bug. Sorry about that.

Would you be okay with sending me the modules and groups text files so that I can do some testing and fix this?

Thanks,

Iva

--
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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[Iva Veseli]

No problem! :)

I was able to reproduce your error in anvi’o v7. Luckily, it appears to have already been fixed in the main development code. 

You could install the development version of anvi’o in a new condo environment by following the instructions here:https://merenlab.org/2016/06/26/installation-v2/#5-follow-the-active-development-youre-a-wizard-arry

And then you would be able to run the enrichment with these files without problems. The command will look slightly different due to Meren's recent update to this code (https://github.com/merenlab/anvio/pull/1742) which split the different enrichment scenarios into three different programs. The new program name that you will need to use is `anvi-compute-metabolic-enrichment`, but it works just the same as anvi-compute-functional-enrichment used to, with the -M and -G parameters. :)

Please let me know if I can be of any further help!

Iva

-------------------------------------------------

Iva Veseli (she/her)
Graduate Student, Meren and Jabri Labs
Biophysical Sciences Program
University of Chicago

On Jun 4, 2021, at 09:54, Herdís <herd...@gmail.com> wrote:

Wow, thanks a lot for the super quick reply!

Sure, here they are. 

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[Herdís]

Thanks, I'll try that :)