search

KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
Other
40 stars 15 forks source link

Fix Issue#349 #356

Closed Sidduppal closed 3 weeks ago

Sidduppal commented 5 months ago

median_completeness is being set to NA when filtered_df is empty. Which is causing the TypeError: boolean value of NA is ambiguous error reported in issue#349. Setting median completeness to 0 when it's NA seems to resolve this without causing any more bugs.

chasemc commented 4 months ago

@Sidduppal or @jason-c-kwan can you create a fresh conda env using this commit? It's taking an incredibly long time to solve on my computer

Sidduppal commented 4 months ago

@chasemc It took about 7 min for the environment to solve and create using mamba. However, the following tests are failing as mentioned before:


FAILED 😰  tests/unit_tests/test_recursive_dbscan.py::test_taxon_guided_binning - autometa.common.exceptions.BinningError: Failed to recover any clusters from dataset
FAILED 😰  tests/unit_tests/test_recursive_dbscan.py::test_get_clusters[hdbscan] - TypeError: boolean value of NA is ambiguous
FAILED 😰  tests/unit_tests/test_recursive_dbscan.py::test_recursive_dbscan_main - SystemExit: 204

@samche42 mentioned that she got pretty reasonable MAGs after using the fix.