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[JoyLiu19]

Dear nselem,
Hi! I recently have installed CORASON in conda just like described in Remove Docker dependency #2，and when I ran the EXAMPLE, I got the same problem as Cannot get results - even with the example #3. I tried to change first line of 3_Draw.pl, but it didn't work. So I wonder if you can give me some help, thank you so much!
ps: I'm using it on the Server with Ubuntu 22.04 LTS (GNU/Linux 5.15.0-40-generic x86_64)

[nselem]

Sure, please let me know If you have the "input files" this is the first corason step, then the 3_draw is just the drawing script.

[JoyLiu19]

Dear nselem,
Yes, I have the "input files". I downloaded the CORASON file in my Server based on your comments in #2 ( git clone https://github.com/nselem/corason.git) and this step ran well.But I stuck in next step, the environment creation (conda env create -f corason.yml ). Fortunately, I successfully created the environment based the comments that under yours and installed the dependencies . when I ran the EXAMPLE for testing whether the installation is correct (CORASON/corason.pl -q ctg2_515.query -rast_ids Example.Ids -s 501926 -conda), I got the same error as #3. Waiting for your reply.
yours sincerely
Joy

[nselem]

Do you have time for a meeting to see your problem? And then we can post here the solution. What about Monday 8:00 am MX time

[JoyLiu19]

That's great to schedule a meeting! Monday 8:00 am MX time is OK. China can only attend the meeting but not book it in Zoom app, could you please book a meeting in Zoom?

[nselem]

Please send me an email at [email protected], maybe we can do it tomorrow at the same time, and I will send you the zoom link.

[JoyLiu19]

Thanks for helping me to through it. And now I'll give an explanation to show how to solve my problem.
The reason for my error is the amount of my input data are too much, and Professor Nelly suggested I can start with small data and gradually add more. So I decreased the amount of my own data to 10, the Error successfully got solved. Therefore, if anyone else with the right format input but still get error, maybe you need to think about whether the number of your input data is too much. Decreasing your data is a useful method to solve it, and you can gradually add more data until there is failed, then the 'bad genomes' need to remove, adding new genomes to go on your process.
I wanna thank you again Professor Nelly!

[nselem]

Some times, there is a genome of bad quality that ruins the alignment, then the tree is empty and also CORASON output. Start with a smaller number of genomes is a good idea!

[Mohsin0911]

if someone is looking this , please help me am also getting same issues, [email protected]

[nselem]

Hello, ¿did the test set run? ¿Which is your operative system? Could you describe a little more your input data, the directory where they are, and how did you install corason?