how can I run the catastrophy program?
1
0
Entering edit mode
27 days ago
pavelasquezv ▴ 20

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'
linux catastrophy • 308 views
ADD COMMENT
0
Entering edit mode
27 days ago
Mensur Dlakic ★ 14k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Many thanks for your help

ADD REPLY

Login before adding your answer.

Traffic: 2189 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6