ccpnmr/bin/lib/CcpNmrAnalysis: line 1: ../../miniconda/bin/python: No such file or directory

Analysis Version 3
1

Hi, I’m getting this error when trying to run any executable in ccpnmr/bin/ :

ccpnmr/bin/lib/CcpNmrAnalysis: line 1: ../../miniconda/bin/python: No such file or directory

but such file is in the right directory.

Version 3.1 and 3.2.2 , both for Linux Ubuntu 20.04.

Any clue or tip?

Thank you!

2

Hi,

the first thing that springs to mind is something that we have seen on Windows, but it could be that the same can happen on Linux. It is that the file browser makes it look as though the .zip file has been unpacked when actually it hasn’t.
I’m sorry if this sounds a bit basic, but we have seen this on several occasions, so it just worth making sure that you have definitely done the extraction.

From what you say about the file being present, it suggests that you haven’t changed any directory names which could otherwise be a problem.

On other operating systems we sometimes have issues with the OS or anti-virus software blocking executables ‘which have been downloaded from the internet’ from being run or extracted, but I’m assuming that with Ubuntu that wouldn’t be the case.

Can you go to the ccpnmr/miniconda/bin directory on the command line and run python from there with?:

./python

Vicky

3

Thanks for the fast answer!

Well, I checked, .zip files was extracted correctly, with permissions, OK.

Runing python from ccpnmr/miniconda/bin directory

returns:

./python: line 1: python3.10: command not found

But python3.10 file is in the right place, executable permission.

Runing python3.10 from ccpnmr/miniconda/bin directory
returns the correct python version info and prompt >>>

Any clue?

BTW, normally, to run the program, one need only to extract .zip file and run a command, like ./assign, right? Or do I need to install or source some file?

Thank you!

4

So it looks as though possibly the symbolic links are not being implemented properly after the unzipping. If you go to the miniconda/bin directory and do

ls -l

then you should be able to see whether the symbolic links have been set up or not. If not, then some of the “files” should be blank / 0 kb in size.

If that is indeed the case, then you will need to work out why your OS isn’t creating the symbolic links after unzipping. I’m afraid we can’t help you with that bit. Is your computer managed by IT who can help you with what is possibly intended to be a “security” feature?

Vicky

5

Thank you! It was that! Somehow ARK extracted the .zip file creating regular files instead symbolic links. So using unzip command extracted files correctly.
But I got another error, I’ll open another thread.

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