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caporaso-lab / sourcetracker2

SourceTracker2
BSD 3-Clause "New" or "Revised" License
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Error: No such option: --per_sink_feature_assignments #138

Open claireewilliams opened 3 years ago

claireewilliams commented 3 years ago

Hello!

I have been using ST2 to calculate sources for each of my sink samples and it's been great. However, I wanted to access the output of each feature's contribution with the --per_sink_feature_assignments flag, but I'm getting this error: Error: No such option: --per_sink_feature_assignments

it's also not listed under the --help flag.

Is the --per_sink_feature_assignments flag still functional? Is there another option?

Thanks!

KMKemp commented 3 years ago

I was having the same issue. Did you see this response? https://github.com/biota/sourcetracker2/issues/101#issuecomment-377409240

I was able to use the --per_sink_feature_assignments option after the following re-installation:

conda create -n st2 -c biocore python=3.6 numpy scipy scikit-bio biom-format h5py hdf5 seaborn
conda activate st2
pip install https://github.com/biota/sourcetracker2/archive/master.zip

This command worked with tiny_test data sourcetracker2 -i otu_table.txt -m map.txt -o example5/ --jobs 5 --per_sink_feature_assignment

claireewilliams commented 3 years ago

Thanks so much!!! I appreciate it, @KMKemp