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harmslab / topiary

Python framework for doing ancestral sequence reconstruction
MIT License
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seed-to-alignment unable to retrieve proteome for key species #39

Open benclifton opened 1 year ago

benclifton commented 1 year ago

I attempted to generate an alignment based on four proteins: a pair of paralogous proteins from human and Arabidopsis thaliana.

This worked until reciprocal BLAST, where topiary was unable to retrieve the Arabidopsis proteome. It seems like topiary selected a genome assembly without an associated proteome, rather than the reference genome.

Following the instructions in the error message, I added a 'recip_blast' column to 01_initial-dataframe and tried restarting the pipeline, but I received the same error.

I'm not sure how general this problem might be, but it might be worth looking into.

Input csv file: test_topiary_NRAMP.csv

Output from first run: terminal_output_1.txt

Edited version of 01_initial-dataframe: 01_initial-dataframe.csv

Output from second run: terminal_output_2.txt

s-pew commented 9 months ago

I am having a similar problem. Was there a resolution to this issue? Thanks!