balabanmetin/uDance

error in rule stitch

Opened this issue · 6 comments

Haicai3782 commented

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

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

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

balabanmetin commented

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

balabanmetin commented

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

balabanmetin commented

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