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biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis
BSD 3-Clause "New" or "Revised" License
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Plugin error from songbird #147

Closed brunobohn7 closed 3 years ago

brunobohn7 commented 3 years ago

I've followed the miniconda/qiime2/songbird installation tutorials, but I continuously run into the error when running the "qiime songbird multinomial" command in the Redsea tutorial:

Plugin error from songbird: 'DataFrame' object has non attribute 'to_dense'

Any idea what could be going on or how to fix it? Thanks!!

gibsramen commented 3 years ago

Hi @brunobohn7. Do you know what version of pandas you are using? I believe the DataFrame.to_dense was removed in one of the recent releases.

brunobohn7 commented 3 years ago

Thank you for the quick response! I believe I am using version 1.1.5?

I've attempted running the following conda install pandas==0.25.3, which I found in #128 , but to no avail. Granted, I am not well versed coding, so it is very likely that I ran it improperly.

gibsramen commented 3 years ago

Interesting. Are you using a QIIME2 environment? If so, which version (i.e. 2020.11)?

brunobohn7 commented 3 years ago

I am using QIIME2, yes. Version 2020.11, which I installed within a Conda environment.

mortonjt commented 3 years ago

@brunobohn7 , maybe try installing qiime2 version 2020.6? This was the last known version of qiime2 that was compatible with songbird.

If that works, I'll add a note to the readme to note this.

brunobohn7 commented 3 years ago

@mortonjt I attempted installing version 2020.6 and it did work! Thank you and @gibsramen so much! Note: I deleted Miniconda and qiime2, and re-installed them all, just to be sure.

mortonjt commented 3 years ago

Great, I'm glad that its working! Thank you for raising this issue.