Comments (9)
Adding this back to Triage so It doesn't get lost because a user noticed on the forum today. Forum ref
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Oh, it may be the unifrac
package adding this actually.
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Thanks @mestaki, that's super strange, we'll need to reproduce this on our end, as it doesn't really make sense that this would happen.
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I think you may be right, I vaguely remember arriving at the same conclusion, I think default unifrac changed at that release to the faster one?
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Hi @mestaki! Thanks for reporting this - I was able to reproduce on my end using 2023.7. This will be a 'good first issue' candidate for a new RSE1 we have joining the team in a few weeks, so I'm going to add some additional details below for their troubleshooting.
Steps to reproduce this issue:
- Install/activate a QIIME 2 environment that is >2022.8 (I used 2023.7)
- Grab sample metadata and feature table/rooted tree artifacts from the Moving Pictures tutorial.
- Run
qiime diversity-lib faith-pd
using the feature table and rooted tree artifacts. - Unzip the resultant artifact, and open the
alpha-diversity.tsv
file within the data directory.
The #SampleID value will be present as the column name above the sample IDs in this table.
Another way to reproduce this issue would be to run qiime diversity core-metrics-phylogenetic
using the metadata and artifacts listed above, and then unzipping the faith-pd artifact that is one of the outputs from running this pipeline. The results will be the same, since this is using the same underlying method.
The #SampleID value should be removed, so that there is no column header for the sample IDs.
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This is perfect for a Good First Issue if we are doing those
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Turns out this one is a bit trickier than we initially anticipated - notes from an old pairing session can be found on this branch for reference. We will address this when @cherman2 and I are back from Europe!
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We will address this issue in our next release, so I am moving this to our 2024.10 release project board.
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This has been fixed, thanks @mestaki for reporting! If you need the updated functionality prior to our next release (2024.10) you can install a development environment once this weekend's new environment files are built.
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Related Issues (13)
- add unit tests of scipy-based qualitative alpha and beta diversity metrics HOT 1
- beta-phylogenetic-alt: psutil(logical=False) reports too few CPUs on EC2 HOT 5
- "Hand-build" test data for weighted unifrac HOT 1
- ENH: refactor test data to run through the QIIME 2 Framework
- Reduce decorator/decorated function coupling in _util._disallow_empty_tables()
- Possible patching bug/maintainability concerns in `test_util.py`
- TODO: update Faith's PD method to use unifrac-based impl HOT 1
- Remove psutil patches from `test_util.py` "through-the-framework" tests HOT 1
- ENH: Provide dispatch functions for q2-diversity
- Allow Bray-Curtis to accept Relative Frequency Data HOT 1
- beta-phylogenetic-meta-passthrough: work with relative frequency and presence/absence table
- Alpha diversity operates on dense feature tables
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