Tree file could not be parsed
josenikhid97 opened this issue · comments
Hello !
I was running a dataset with correct file names , correct file location and also data inside the files . ./rd -- msa --tree and the tool shows an error " There was an error during processing , Tree file could not be parsed ". is there any way to overcome this problem. I am also attaching the error.
Thank you in advance
Would it be possible for for you to send the tree? If that isn't possible, try to open the tree in another program like dendroscope or treefig, to make sure it is properly formatted.
sure, i can send you the tree file,but it is large so i am not able to send you but it seems the format is correct because the newick format is the end product of one of the tool i am using. so i am sending you the screenshot of the file format.
newick format is the end product of one of the tool
Unfortunately, newick isn't super standardized, so this isn't a guarantee.
I can't reproduce the problem based on the screenshot you sent me, so I think you are going to have to send me the tree file in order for me to solve the problem.
Alternatively, you could switch to the coraxlib branch of RootDigger, and try with that version. That branch has a parser which might give much better error messages.
any possible way of sending you the tree file ?, i am sending the google drive link of the tree file and fasta file
https://drive.google.com/file/d/1YiLcVRTpJEVtkp9fNTrGlN9rJzDUcqZb/view?usp=sharing
https://drive.google.com/file/d/1LE6JwcLWM7UWquUsA1bnqux7SkkAf2pl/view?usp=sharing
please let me know the problem
Thank you for the tree file and the alignment. I am on vacation at the moment, so I didn't get a ton of time to look at this. I don't know what is wrong with the parsing when using the master branch, but when using the coraxlib branch everything seems to work fine (I didn't let it run very long, but it never gave an error after about 5 min).
The short story is that this has convinced me to finally just update the master branch to use coraxlib. This should fix your issue. Let me know if it doesn't.
sure , thank you . how to run on coraxlib, do i have to use any flag on the terminal command ?, or is it the general command ?
Sorry, I should have been clearer. v1.8.0 of RootDigger uses coraxlib by default. You just have to pull the new changes and rebuild the binary.
Great !!
Thank you so much for your time and have a great time spending your vacation
I'm not sure how large it is, but compressing the file (with zip or 7zip) should reduce the size of the file quite a bit. From there, maybe it is possible to upload it to google drive and send me a link?
This ticket is several months old with no reply, I am closing the issue