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raphael-group / decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
BSD 3-Clause "New" or "Revised" License
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"Skipping mutation" warning still there with new state trees file #21

Closed lbresadola closed 2 years ago

lbresadola commented 2 years ago

Dear all,

thanks for creating DeCiFer!

I am having issues with the warning "UserWarning: Skipping mutation ###: State tree file does not contain state trees for the set of copy-number states that affect mutation ###." in the DeCiFer runs. I created new state tree files with generatestatetrees for two patients I am analyzing and I re-ran DeCiFer with them. However, while for one patient I don't get the warnings anymore, for the second patient the warnings are still there, although not for all SNVs for which they appeared before (168 SNVs, instead of 231). I tried to increase -maxCN and -maxXY to extreme numbers (50), but the state tree file didn't change and this didn't solve the problem.

Do you know why this could happen? Is there any other parameter in generatestatetrees that should be adjusted?

The DeCiFer input files were created with vcf2decifer.py and these are the commands I used (both in v2.0.2 and v2.1.0): generatestatetrees cn_states.txt > /my_path/new_state_tree_file.txt

decifer -p /my_input_path/decifer.purity.tsv /my_input_path/decifer.input.tsv --jobs 12 -K 15 --record --printallk --restarts 100 --statetrees /my_path/new_state_tree_file.txt --output /my_output_path/patient_XX_new_state_tree_K15

Thanks a lot for your help! Best,

Luisa

brian-arnold commented 2 years ago

Hi Luisa, Hmmm interesting... if they aren't too large, could you post the following files here for me to peek at: cn_states.txt /my_input_path/decifer.purity.tsv /my_input_path/decifer.input.tsv

I have a guess at what might be occurring, but it'd be best if I could do some digging on my end. Sincerely, Brian

lbresadola commented 2 years ago

Hi Brian,

thanks for your quick reply! Here are the files (it is WES data, so they are small). I had to convert the .tsv files to .txt, since .tsv format is apparently not supported.

Best,

Luisa

cn_states.txt decifer.input.txt decifer.purity.txt

brian-arnold commented 2 years ago

Hi Luisa, Gryte figured out what was causing the issue. We fixed the code here on github and are in the process of making a new conda release, but until that comes out (which will hopefully be in the next day or so) you could always do a custom install of the main branch. I'll let you know as soon as I do when the new version is released! Sincerely, Brian

lbresadola commented 2 years ago

Great! Thanks a lot Brian and Gryte!

brian-arnold commented 2 years ago

FYI the new version should now be available.