Sourcetracker 2 Barplot Error

Community Plugin Support
1

Hello,

I am having an issue with the Sourcetracker2 plugin and having trouble figuring out the issue based on the error code and the limited information out there on the plugin. I run the following command and it generates an output.

Mapping file: Mapping_file_update.txt (5.4 KB)
Feature table: feature-table-source-sink.qza (1.0 MB)

qiime sourcetracker2 gibbs --i-feature-table Sourcetracker2/feature-table-source-sink.qza --m-sample-metadata-file Sourcetracker2/Mapping_file_update.txt --p-source-sink-column SourceSink --p-source-column-value source --p-sink-column-value sink --p-source-category-column Env --p-loo --p-jobs 10 --output-dir Sourcetracker2/loo

Outputs:
mixing_proportion_stds.qza (106.5 KB) mixing_proportions.qza (106.5 KB) per_sink_assignments_map.qza (105.1 KB) per_sink_assignments.qza (501.6 KB)

I then run the following command to generate barplots and receive an error.

qiime sourcetracker2 barplot --i-proportions Sourcetracker2/loo/mixing_proportions.qza --m-sample-metadata-file Sourcetracker2/Mapping_file_update.txt --o-visualization Sourcetracker2/loo/proportions.qzv

Plugin error from sourcetracker2:

'DataFrame' object has no attribute 'ids'

Debug info has been saved to /var/folders/67/6dbph7ys1d3240bqc4wgn7380000gp/T/qiime2-q2cli-err-1m63fsaw.log

This might just be simple user error as I mentioned but looking in the log file, it doesn't provide much additional info besides the displayed error message. Would any of the Sourcetracker2 or FEAST contributors be able to take a look at this?

Thanks for the support and let me know if additional information/files are needed,

TNT

2

Hi!
I am having the exact same error message when I try to do the same command. Did you figure out what needed to be done?

Thank you :slight_smile:

3

Hi Todd_Testerman,
I am having exactly the same issues to create Sourcetracker Barplot. Similar to your problem, I also got 4 output .qza files and then failed to create barplot. Do you find the ways to figure it out?

4

Hi @Audrey_Anne and @shak71 ,

Unfortunately I did not get this figured out and haven't heard anything from the plugin developers. It's been almost a year since I tried so that's too bad there still seems to be a lingering issue you both are experiencing. It may be worth posting within the help sections of the FEAST or Sourcetracker 2 GitHub repos to get someone's attention.

Best of luck.

TNT

1 Like
5

Thanks @Todd_Testerman for your quick response!!!