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`anvi-get-enriched-functions-per-pan-group` requires the following packages:
`tidyverse`
`magrittr`
`qvalue`
The question is how do we deal with that?
1. We can install these as part of the a…
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Currently genomes storage is generated from internal and external genomes files, and is used for the pangenomic workflow. Unfortunately due to my oversight at the beginning it has some shortcomings:
…
meren updated
4 years ago
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Hi there!
I'm running your pangenome workflow on some test data and I keep hitting an error when diamond is creating the search database. Here's the result of a self test:
```
(anvio-5.1) $ anv…
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While this issue contains specific requests for @ozcan and @ekiefl down below, anyone who wish to test the new taxonomy branch can follow this recipe.
It will require you to switch to `anvio-taxono…
meren updated
4 years ago
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Hi there,
this is a general comment on potential future developments not related to a specific anvi'o version, or bug.
I recently realized that the pangenomic workflow of anvi'o could be improved …
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Hello,
I'm trying to get pangenomic analysis for Lactobacillus plantarum from NCBI, then follow the tutorial here (http://merenlab.org/2019/03/14/ncbi-genome-download-magic/#processing-ncbi-genomes)
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fetyj updated
4 years ago
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When using `--min-num-bins-gene-occurs` in `anvi-get-sequences-for-hmm-hits` with external genomes then you get this message:
```
Config Error: OK. Well. This is awkward. You have like 1 bins, eh?…
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If I try:
```
anvi-self-test --suite pangenomics
````
I will get the following output. The error is at the bottom.
```
:: Output directory ...
/var/folders/86/v68d1x9s59128vx4pr1kl…
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I get the following error:
```
raceback (most recent call last):
File "/Users/alonshaiber/github/anvio/bin/anvi-get-sequences-for-gene-clusters", line 154, in
main(args)
File "/Users/alo…
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I tried to test pangenomic workflow with `anvi-self-test --suite pangenomics` and got an error. Based on log-file, it was appeared due to the use of deprecated static method `pd.DataFrame.from_csv`.
…