Autometa
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KwanLab
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://github.com/KwanLab/Autometa/blob/5e3250cfaa1fb9ec0e6361be1ab6aadc619f73a0/autometa/binning/recursive_dbscan.py#L190 I am getting this 'NA' error - ``` ... site-packages/autometa/binning/recursive_dbscan.py", line 190, in recursive_dbscan if median_completeness >= best_median: File "missing.pyx", line 419, in pandas._libs.missing.NAType.__bool__ TypeError: boolean value of NA...
`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](https://github.com/KwanLab/Autometa/issues/349). Setting median completeness to 0...
Replace nf-core code of conduct template with Contributor Covenant template https://www.contributor-covenant.org/version/2/1/code_of_conduct/code_of_conduct.md
autometa-binning-summary throw error because of different expectation for .to_csv - I assume this is a pandas version problem I have? per https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.to_csv.html which changed after 1.5.0 but the env requirements...
Docs: Fix conda command ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code...
# Current Behavior Error message about ncbi server connection but this is a marker download (raw.github.com download) ``` File "/bigdata/operations/pkgadmin/opt/linux/centos/8.x/x86_64/pkgs/autometa/2.2.1/env/lib/python3.10/site-packages/autometa/config/databases.py", line 204, in get_remote_checksum raise ConnectionError("Cannot connect to the NCBI...
Fix Biopython deprecation warning: ```console /usr/share/miniconda/envs/autometa/lib/python3.8/site-packages/Bio/SeqUtils/__init__.py:144: BiopythonDeprecationWarning: GC is deprecated; please use gc_fraction instead. ``` Instead of `SeqUtils.GC` use `SeqUtils.gc_fraction` Found in logs here: https://github.com/KwanLab/Autometa/actions/runs/4994350221/jobs/8944784711?pr=325 `SeqUtils.gc_fraction` implementation is here: https://github.com/biopython/biopython/blob/8293b7382081b8f6cc135638a956a7736633115e/Bio/SeqUtils/__init__.py#L48-L136...
There are some files that don't exist for all of the example datasets which causes the script to fail: ``` Access denied with the following error: Cannot retrieve the public...
# Current Behavior Since kingdoms is defined multiple times in workflows/autometa_flagged.sh, it is easily missed if a user wants to change the value of this variable ## Steps to Reproduce...
