udem-lbit / coretracker Goto Github PK

Hi @maclandrol,

Sorry to bother you again.
I am having another problem with the CoreTracker.
The program can run but it seems to stop at a certain point when predicting the possible codon reassignment. The run has never finished even after a few days.
The only error message that I received was:

ETE: cannot connect to X server

Do you know how to resolve this issue?

Many thanks

Hi!

I am interested to use the CoreTracker program, but encountered some problems during the installation.
I have followed the instruction for conda installation but was given this error message:

Fetching package metadata: ..........
Solving package specifications: ....

The following specifications were found to be in conflict:
  - coretracker
  - mkl_fft (target=mkl_fft-1.0.15-py27ha843d7b_0.tar.bz2) -> numpy >=1.11.3,<2.0a0
  - mkl_random (target=mkl_random-1.1.0-py27hd6b4f25_0.tar.bz2) -> numpy >=1.14.6,<2.0a0
Use "conda info <package>" to see the dependencies for each package.

I have tried to reinstall the numpy and scipy as recommended, but the problem still persist.
Do you know how to troubleshoot this?

Thanks!

Hi @maclandrol,
I am having an issue while running CoreTracker.
I am getting the program to run successfully, however, I noticed that it consistently filters out the sequences of interest to me. I input sequences from at least 70 different species, but the only ones that appear to be missing from the output codon_data files are the ones that I care the most about. While running, CoreTracker tells me "DEBUG:root:Non-uniform sequence in sequences and tree. The tree will be pruned." So I'm assuming that my sequences of interest are pruned out. I would like to know what constitutes "non-uniform" and if there is a way that I can keep them from being removed? I'm aware that those sequences are particularly divergent from the rest...which is exactly why I want to use CoreTracker on them!

Thank you for your help,
Nicole

Cannot install using pip without -e.

muscle, mafft and hmmer package are not checked during installation. Download and install them directly with setup.py