how can I run the catastrophy program?

Question

[pavelasquezv]

Hi people,

I am new to bioinformatics

I'm trying to run a catastrophy program, but I get the following error.

Can someone help me? please

    /root/.local/bin/catastrophy  -f dbcan -o my_catastrophy_results.csv mp1.txt

Traceback (most recent call last):
  File "/root/.local/bin/catastrophy", line 8, in <module>
    sys.exit(main())
  File "/root/.local/lib/python3.7/site-packages/catas/main.py", line 84, in main
    with open(data.model_filepath(args.model_version), "rb") as handle:
FileNotFoundError: [Errno 2] No such file or directory: '/root/.local/lib/python3.7/site-packages/catas/data/model_v8_20200114.npz'

Answer 1

[Mensur Dlakic]

The error message tells you that it can't find a certain model file, which is most likely a part of program's installation. Re-installing the program would probably fix it.

By the way, not a good idea to install conda packages as sudo/root, or to run them like that. Most people will tell you to run programs as a regular user.

[pavelasquezv]

Thanks very much for your reply

I am runing the program on google colab. I Re-installing the program but does not work. Would you like to give me another suggestion?

This is the script in google colab:

https://colab.research.google.com/drive/1Agg7MpllsT68duehX5x1IoiyqJHv_kPo#scrollTo=zyOk0Mxcp6J5&uniqifier=1

[Mensur Dlakic]

I would like to give you a different suggestion, as long as you give me a different error message.

There is nothing ambiguous about this error message: No such file or directory: '/root/.local/lib/python3.7/site-packages/catas/data/model_v8_20200114.npz'. The program can't find one of the files it needs, and it won't run. It's kind of like a baker not being able to make a quiche without eggs. You can look for other solutions, but it doesn't work without eggs. Same for your case.

[pavelasquezv]

Ok Mensur, I understand, the problem is in the installation of the program. I will try to install everything again to see if I can resolve.

[pavelasquezv]

Many thanks for your help