Problem with running Songbird

Community Plugin Support
1

Hello,

I'm having an issue with running Songbird in Qiime2. I was able to follow the steps in "2. Using Songbird through Qiime2" as detailed in the following link (GitHub - biocore/songbird: Vanilla regression methods for microbiome differential abundance analysis). I successfully installed Songbird and imported the necessary data. However, when actually running Songbird, I come across an error that reads:

Plugin error from songbird:

  • 'DataFrame' object has no attribute 'to_dense'*

Debug info has been saved to /tmp/qiime2-q2cli-err-br8wsjj0.log

I'm unsure how to resolve this 'DataFrame' issue. I've attached a copy of the error log in a txt. file below as a reference:

qiime2-q2cli-err-br8wsjj0.txt (1008 Bytes)

Is there a potential solution to this issue? I am very new to using Qiime2/Songbird and bioinformatics in general, so additional details and instructions would very much be helpful. I am using Qiime2 in Linux on VirtualBox on a Windows PC. I have Qiime2 2020.11 installed.

Best,
Idmah72

2

Hi @idmah72,

I think this is a version conflict underlying the plugin. As a temporary solution, Songbird should be compatible with qiime2-2020.8.

Best,
Justine

3 Likes
7

Hi, I also have the same problem, when I run Songbird plugin in Qiime2 2020.11 and 2021.02, although I have not test in v2020.08.

Best,

Wan

8

Hi @williamshell, welcome to :qiime2:!

If you read the Songbird documentation you'll see the following warning:

First, you'll need to make sure that QIIME 2 is in between (version 2019.7 and 2020.6 ) is installed before installing Songbird.

If memory serves this has to do with an incompatibility some dependencies between the latest versions of base QIIME and Songbird.

1 Like