[BUG] anvi-script-visualize-split-coverages error with SNV data

mschecht commented 3 years ago

Short description of the problem

anvi-script-visualize-split-coverages is unable to produce a pdf when given SNV data.

anvi'o version

$ anvi-self-test --version

Anvi'o .......................................: hope (v7-dev)

Profile database .............................: 35
Contigs database .............................: 20
Pan database .................................: 14
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 1

System info

macOS Big Sur 11.2.3

Detailed description of the issue

anvi-script-visualize-split-coverages is unable to produce a pdf when given SNV data via the flag --snv-data. However it works perfectly if no SNV data is provided.

You can produce this by following the anvi-script-visualize-split-coverages tutorial until the part where it describes visualizing SNVs.

Thanks in advance for the help!

meren commented 3 years ago

I just run the entire set of commands in that tutorial and everything worked for me :/

mschecht commented 3 years ago

Thanks for running it on your end! I unfortunately am still getting the same error as above. Maybe it's my R version?

meren commented 3 years ago

Perhaps. Mine is 3.5.1.

nvpatin commented 2 years ago

@mschecht did you ever resolve this issue? I am having the same problem generating split coverages with SNV data.

nvpatin commented 2 years ago

I was able to solve it by downgrading R to version 3.5.1, but I got the following warning: "Warning message: As of rlang 0.4.0, dplyr must be at least version 0.8.0.

dplyr 0.7.8 is too old for rlang 0.4.5.
Please update dplyr with install.packages("dplyr") and restart R.

Nevertheless it created the PDF so for now I think that is the best solution.

merenlab / anvio