Error while running CPAT

Question

[kousi31]

Hi all, I am running CPAT to find the coding potential of nucleotides. I used the following commands. But I am getting an error while trying to run make_logitModel.py

make_hexamer_tab.py -c random_cds.fa  -non_coding.fa >hexamer.tsv
make_logitModel.py  -x hexamer.tsv -c random_cds.fa -n non_coding.fa -o logit

R/bin/exec/R: error while loading shared libraries: libicuuc.so.56: cannot open shared object file: No such file or directory

when I run ldconfig -p | grep libicuuc I am getting following output.

    libicuuc.so.60 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libicuuc.so.60
    libicuuc.so.60 (libc6) => /usr/lib/i386-linux-gnu/libicuuc.so.60
    libicuuc.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libicuuc.so

I am not familiar with software installations in linux. Kindly help!

[grant.hovhannisyan]

don't know how to solve this exact dependency, but you can try installing cpat using conda, it should solve all dependencies https://anaconda.org/bioconda/cpat

[kousi31]

I am getting this error in bioconda

Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

[grant.hovhannisyan]

have you tried installing in a new environment?

[kousi31]

I tried downloading the source "CPAT-2.0.0.tar.gz", and running from the "bin" and still got the error

[kousi31]

I have downloaded CPAT-1.2.4
It requires Python2.7
I have installed Python-2.7 in /usr/src/Python-2.7
Python 3.7.3 is in /home/d/miniconda3/bin/python

I tried to run alias python=/usr/bin/Python-2.7 before running cpat.py from bin directory of CPAT-1.2.4. But still the software is using python 3.7.3.

Can you please tell me how to direct the software towards Python2.7.

Thank you!

[grant.hovhannisyan]

it seems you did´t use conda.

first install miniconda (it is a package manager) https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html

when installed, create a new environment, for example: conda create -n env_cpat

activate the environment:

conda activate env_cpat

then install cpat:

conda install -c bioconda cpat

then try running cpat. hopefully it works

[kousi31]

Thank you. It worked.

[grant.hovhannisyan]

good. then you can accept my answer to close the thread