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balabanmetin / uDance

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error in rule stitch #5

Open Haicai3782 opened 8 months ago

Haicai3782 commented 8 months ago

I used the "tree" option with referenced backbone.nwk and the alignments of 133 genes including 142 species.It occur some errors. some log.file are here. And weired,If I run the udance with random tree(generated randomly from the species),it can run successfully. no backbone tree also can run successfully. I don't know whether this is a problem with my backbone or something else.

udance.log 2023-10-20T144057.410577.snakemake_error.log config (1).yaml.txt

Do you have any idea to figure out this issue? Thank you very much.

balabanmetin commented 8 months ago

It's not an error I have seen before. My recommendation is to delete line 120:

assert len(astral_tree_par.root.children) == 3

from /home/fp23165/software/uDance/uDance/stitch.py and rerun the stitch step. This assert might be redundant. By the way, wou won't need to rerun the full pipeline, only the last step.

Haicai3782 commented 8 months ago

Hmm,it doesn't work.still get same errors

balabanmetin commented 8 months ago

would you like to share the new error message with me?

Haicai3782 commented 8 months ago

here is the new log 2023-10-26T164224.357026.snakemake.log

udance.log

here are the data I used.If you want to test,you can use them. https://drive.google.com/drive/folders/1S8aItR60en4mnGM2StWhd8_4KPHsvur-?usp=sharing

balabanmetin commented 8 months ago

Oh I see, it got stuck in another assert down below. I will try to debug it this weekend

balabanmetin commented 7 months ago

I ran uDance twice using the data you shared. I wasn't able to reproduce the error. I am attaching all the files in my successful run. I hope this helps. Thanks for using uDance

https://drive.google.com/file/d/1C4rjy-0MIdwVEAfCPhu1l40Mb6DVw0_v/view?usp=share_link