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Vini2 / phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
https://phables.readthedocs.io/
MIT License
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marker.hmm file broken #53

Closed nikolasbasler closed 4 weeks ago

nikolasbasler commented 1 month ago

Hi,

I installed phables 1.3.2 via conda recently, following the instructions in the docs. phables install and phables test both finished successfully. However, the marker.hmm file, located in mambaforge/envs/phables/lib/python3.11/site-packages/phables/workflow/../../databases/marker.hmm only contains one line 404: Not Found, causing phables runs on my data to crash. The output/logs/smg_scan_hmm_err.log reads:

Error: File format problem in trying to open HMM file /vsc-hard-mounts/leuven-data/341/vsc34111/mambaforge/envs/phables/lib/python3.11/site-packages/phables/workflow/../../databases/marker.hmm. Format tag is '404:': unrecognized. Current H3 format is 'HMMER3/f'. Previous H2/H3 formats also supported.

I deleted the marker.hmm file and re-ran phables install, but that just regenerates the file with the same content.

Any help would be appreciated.

Thanks, Nikolas

Vini2 commented 4 weeks ago

Hi @nikolasbasler,

Thanks for your interest in Phables.

The path to the marker.hmm file has been updated. I will fix it ASAP and put out a new release.

Thanks for bringing this to my attention.

nikolasbasler commented 4 weeks ago

Cool thanks! Will you also update the conda recipe?

Vini2 commented 4 weeks ago

Hi @nikolasbasler,

The updated conda version is now live at https://anaconda.org/bioconda/phables. Please let me know if there are any further issues.

Thanks!

Vini2 commented 4 weeks ago

Closing this issue after fixing it. Please re-open if needed.