Exporting chemical shift list for TALOS+

Marta · 10 June 2024 14:20

Hi,

I need to export the chemical shift list in a .tab file
Is it possible? If yes how is it done?
If not possible, is there any way to have a prediction of phi and psi backbone torsion angle using a combination of chemical shift assignments for a given residue sequence?

thanks

varioustoxins · 10 June 2024 16:46

Hi If you are looking to use talos you can export to nef and then Use NEF=Pipelines to produce NMRPipe table files for use with TALOS.

NEF=Pipelines can be installed with the install_nef_piplines command inside ccpn or following the instructions on the NEF=Pipelines website GitHub - varioustoxins/NEF-Pipelines: Nef tools

to export talos you would export a nef file [e.g. file_name.nef] and then do

nef talos export shifts --in file_name.nef

then run talos

finally there are various parts of the talos data you can reimport

nef talos import sequence file_name.pred | nef talos import restraints file_name.pred > file_name_talos.nef

etc which will build up a nef file, you can then print tables, export xplor restraints, export to xplor or reimport back into ccpn [currently only works for restraints]

there is a ccpn tutorial here Tutorials - CCPN - Collaborative Computing Project for NMR and some video from our nef workshop online

any questions do come back and ask…

regards
gary

Marta · 11 June 2024 07:42

Thank you very much, Gary
I will try immediately and if there are any problems I will ask you again :)

Marta

Marta · 11 June 2024 08:51

Dear Gary

I tried the things you suggested but I still have problems. Any suggestions?

WARNING: the following plugins failed to load:

nef_pipelines.tools.about
nef_pipelines.tools.chains
nef_pipelines.tools.entry
nef_pipelines.tools.fit
nef_pipelines.tools.frames
nef_pipelines.tools.header
nef_pipelines.tools.peaks
nef_pipelines.tools.save
nef_pipelines.tools.series
nef_pipelines.tools.shifts
nef_pipelines.tools.simulate
nef_pipelines.tools.test
nef_pipelines.transcoders.csv
nef_pipelines.transcoders.echidna
nef_pipelines.transcoders.fasta
nef_pipelines.transcoders.mars
nef_pipelines.transcoders.nmrpipe
nef_pipelines.transcoders.nmrview
nef_pipelines.transcoders.pales
nef_pipelines.transcoders.rcsb
nef_pipelines.transcoders.rpf
nef_pipelines.transcoders.shifty
nef_pipelines.transcoders.sparky
nef_pipelines.transcoders.nmrstar
nef_pipelines.transcoders.talos
nef_pipelines.transcoders.xcamshift
nef_pipelines.transcoders.xeasy
nef_pipelines.transcoders.xplor

the remaining plugins will work but NEF-Pipelines is working with reduced capabilities. The modules
that failed to load and the causes of the problem are listed above please report this to the authors
at github: https://github.com/varioustoxins/NEF-Pipelines/issues

Marta · 11 June 2024 08:52

Dear Gary

I tried the things you suggested but I still have problems. Any suggestions?

WARNING: the following plugins failed to load:

            nef_pipelines.tools.about

nef_pipelines.tools.chains
nef_pipelines.tools.entry
nef_pipelines.tools.fit
nef_pipelines.tools.frames
nef_pipelines.tools.header
nef_pipelines.tools.peaks
nef_pipelines.tools.save
nef_pipelines.tools.series
nef_pipelines.tools.shifts
nef_pipelines.tools.simulate
nef_pipelines.tools.test
nef_pipelines.transcoders.csv
nef_pipelines.transcoders.echidna
nef_pipelines.transcoders.fasta
nef_pipelines.transcoders.mars
nef_pipelines.transcoders.nmrpipe
nef_pipelines.transcoders.nmrview
nef_pipelines.transcoders.pales
nef_pipelines.transcoders.rcsb
nef_pipelines.transcoders.rpf
nef_pipelines.transcoders.shifty
nef_pipelines.transcoders.sparky
nef_pipelines.transcoders.nmrstar
nef_pipelines.transcoders.talos
nef_pipelines.transcoders.xcamshift
nef_pipelines.transcoders.xeasy
nef_pipelines.transcoders.xplor

        the remaining plugins will work but NEF-Pipelines is working  with reduced capabilities. The modules
        that failed to load and the causes of the problem are listed above please report this to the authors
        at github: https://github.com/varioustoxins/NEF-Pipelines/issues

Marta

varioustoxins · 11 June 2024 09:36

that’s really not good these error message indicate there is an installation problem, so sorry we will have debug that first

-1. could you try running nef about and giving me the error trace it gives
0. did you install nef-pipelines via ccpn or pipe?

did you upgrade nef-pipelines to its latest version with the install_nef_piplines script if you used ccpn?
what platform are you running on [windows, max, linux; version and flavour…]
what version do you have, since about is not working you will have to look in the distribution
you should find in there a file called VERSION on the path src/nef_pipelines/VERSION it should be 0.1.75 or 0.1.76

Marta · 11 June 2024 09:47

Dear Gary

thanks for the quick reply.

Yes I upgrade the nef pipelines

I am currently running on Win11

Edizione	Windows 11 Pro
Versione	23H2
Data installazione:	‎18/‎03/‎2024
Build sistema operativo	22631.3593
Esperienza	Windows Feature Experience Pack 1000.22700.1003.0

0.1.76

I installed it thorugh prompt of windows (pipe)

Thanks in advance

varioustoxins · 11 June 2024 09:49

ah I have problems in windows, I will need to look at this… Its currently only guaranteed to work on Mac and linux and you will need a Mac or linux for talos

do you have windows sub system for linux?

Marta · 11 June 2024 09:50

Not yet but I guess I need it right?

Thanks

Marta

varioustoxins · 11 June 2024 09:56

well to run talos you will need to goto another machine [local or nmrbox] it doesn’t run on windows

but wsl should let you run talos locally…

I should have a windows box to test on soon but I don’t currently

Marta · 11 June 2024 09:59

Ok, perfect

Thank you a lot

Marta :)

Marta · 12 June 2024 09:49

Dear Gary,

I tried using Ubuntu (22.04.3 LTS) for the installation, following the steps that you suggested, but the error that I sent you yesterday still remains.

What can I do?

Thanks
Marta

varioustoxins · 12 June 2024 09:59

Hi Marta

did you install it inside ubuntu (via pipe?) run it inside the the ubuntu shell using the version installed inside ubuntu?

regards
Gary

Marta · 12 June 2024 10:02

Yes, I tried that one

varioustoxins · 12 June 2024 11:05

that is very odd maybe we should arrange a teams / zoom / anydesk session and I can have a look at whats going on… I can’t see whats the problem here

what do you get when you type which nef in an ubuntu shell?

regards
Gary

Marta · 12 June 2024 12:40

when I type “which nef” I get /home/marta/.local/bin/nef

(I don’t know if this is a problem, but I use Ubunt in a virtual machine)

Marta

varioustoxins · 12 June 2024 12:47

Hi

That looks right can you let me know which version of ubuntu you are running on, testing is done on ubuntu 22.04

Also if the nef command produces an error could you sent that to me as well [ie whats the text you get if you type nef or nef about in the ubuntu console]

regards
Gary

Marta · 12 June 2024 13:00

Ubuntu version is 22.04.3 LTS and this is the whole error that appears when I type “nef”

marta@marta-VirtualBox:~$ nef

Usage: nef [OPTIONS] COMMAND [ARGS]…

Options:

–install-completion [bash|zsh|fish|powershell|pwsh]

                              Install completion for the specified shell.

–show-completion [bash|zsh|fish|powershell|pwsh]

                              Show completion for the specified shell, to

                              copy it or customize the installation.

–help Show this message and exit.

Commands:

chains - carry out operations on chains

csv - read [rdcs]

echidna - read echidna data [peaks]

entry - carry out operations on the nef file entry

fasta - read and write fasta sequences

fit - carry out fitting operations [alpha]

frames - carry out operations on frames in nef frames

mars - read and write mars [shifts and sequences]

nmrpipe - read nmrpipe [peaks shifts & sequencess]

nmrstar - read NMR-STAR [sequences & shifts]

nmrview - read and write nmrview [peaks, sequences & shifts]

pales - read and write pales/dc [rdcs]

pdbx - read pdb [sequences]

peaks - carry out operations on nef peaks

rpf - write rpf shifts

series - carry out operations on a data series

shifts - carry out operations on shifts [average]

shifty - write shifty [shifts]

simulate - simulate data

sink - read the current stream and don’t write anything

sparky - read sparky files [shifts]

stream - stream a nef file

talos - read and write talos files [shifts & restraints]

xcamshift - write xcamshift for xplor [shifts]

xeasy - read xeasy files [flya dialect: sequence]

xplor - read xplor [sequences, dihedral & distance restraints]

********************************************** error in nef_pipelines.tools.about *************************************************

plugin nef_pipelines.tools.about

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/about.py”, line 9, in

from nef_pipelines.lib.util import get_version

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/lib/util.py”, line 28, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

*************************************************** error in nef_pipelines.tools.chains ******************************************************

plugin nef_pipelines.tools.chains

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/chains/init.py”, line 14, in

import nef_pipelines.tools.chains.clone  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/chains/clone.py”, line 6, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

*************************************************** error in nef_pipelines.tools.entry ******************************************************

plugin nef_pipelines.tools.entry

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/entry/init.py”, line 16, in

import nef_pipelines.tools.entry.rename  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/entry/rename.py”, line 6, in

from nef_pipelines.lib.nef_lib import read_entry_from_stdin_or_exit

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/lib/nef_lib.py”, line 11, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

**************************************************** error in nef_pipelines.tools.fit *******************************************************

plugin nef_pipelines.tools.fit

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/fit/init.py”, line 14, in

import nef_pipelines.tools.fit.exponential  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/fit/exponential.py”, line 7, in

from pynmrstar import Entry, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

*************************************************** error in nef_pipelines.tools.frames ******************************************************

plugin nef_pipelines.tools.frames

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/frames/init.py”, line 16, in

import nef_pipelines.tools.frames.delete  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/frames/delete.py”, line 7, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

********************************************** error in nef_pipelines.tools.header *************************************************

plugin nef_pipelines.tools.header

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/header.py”, line 2, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

*************************************************** error in nef_pipelines.tools.peaks ******************************************************

plugin nef_pipelines.tools.peaks

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/peaks/init.py”, line 16, in

import nef_pipelines.tools.peaks.match  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/peaks/match.py”, line 6, in

from pynmrstar import Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

********************************************** error in nef_pipelines.tools.save *************************************************

plugin nef_pipelines.tools.save

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/save.py”, line 9, in

from pynmrstar import Entry, cnmrstar

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

*************************************************** error in nef_pipelines.tools.series ******************************************************

plugin nef_pipelines.tools.series

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/series/init.py”, line 14, in

import nef_pipelines.tools.series.build  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/series/build.py”, line 11, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

*************************************************** error in nef_pipelines.tools.shifts ******************************************************

plugin nef_pipelines.tools.shifts

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/shifts/init.py”, line 14, in

import nef_pipelines.tools.shifts.average  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/shifts/average.py”, line 7, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

*************************************************** error in nef_pipelines.tools.simulate ******************************************************

plugin nef_pipelines.tools.simulate

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/simulate/init.py”, line 12, in

import nef_pipelines.tools.simulate.peaks  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/simulate/peaks.py”, line 9, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

************************************************ error in nef_pipelines.tools.test **************************************************

plugin nef_pipelines.tools.test

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/tools/test.py”, line 8, in

from nef_pipelines.lib.test_lib import run_and_read_pytest, select_matching_tests

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/lib/test_lib.py”, line 10, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.csv *********************************************************

plugin nef_pipelines.transcoders.csv

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/csv/init.py”, line 16, in

import nef_pipelines.transcoders.csv.importers.peaks  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/csv/importers/peaks.py”, line 12, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

****************************************************** error in nef_pipelines.transcoders.echidna *********************************************************

plugin nef_pipelines.transcoders.echidna

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/echidna/init.py”, line 16, in

import nef_pipelines.transcoders.echidna.importers.peaks  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/echidna/importers/peaks.py”, line 8, in

from pynmrstar import Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************** error in nef_pipelines.transcoders.fasta **********************************************************

plugin nef_pipelines.transcoders.fasta

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/fasta/init.py”, line 18, in

import nef_pipelines.transcoders.fasta.exporters.sequence  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/fasta/exporters/sequence.py”, line 8, in

from nef_pipelines.lib.nef_lib import (

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/lib/nef_lib.py”, line 11, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************** error in nef_pipelines.transcoders.mars ***********************************************************

plugin nef_pipelines.transcoders.mars

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/mars/init.py”, line 24, in

import nef_pipelines.transcoders.mars.exporters.fragments  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/mars/exporters/fragments.py”, line 8, in

from pynmrstar import Entry, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.nmrpipe *********************************************************

plugin nef_pipelines.transcoders.nmrpipe

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/nmrpipe/init.py”, line 19, in

import nef_pipelines.transcoders.nmrpipe.importers.peaks  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/nmrpipe/importers/peaks.py”, line 11, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.nmrview *********************************************************

plugin nef_pipelines.transcoders.nmrview

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/nmrview/init.py”, line 25, in

import nef_pipelines.transcoders.nmrview.exporters.peaks  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/nmrview/exporters/peaks.py”, line 13, in

from nef_pipelines.lib.nef_lib import (

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/lib/nef_lib.py”, line 11, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

****************************************************** error in nef_pipelines.transcoders.pales ********************************************************

plugin nef_pipelines.transcoders.pales

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/pales/init.py”, line 18, in

import nef_pipelines.transcoders.pales.exporters.rdcs  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/pales/exporters/rdcs.py”, line 8, in

from pynmrstar import Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************** error in nef_pipelines.transcoders.rcsb **********************************************************

plugin nef_pipelines.transcoders.rcsb

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/rcsb/init.py”, line 15, in

import nef_pipelines.transcoders.rcsb.importers.sequence  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/rcsb/importers/sequence.py”, line 7, in

from nef_pipelines.lib.sequence_lib import sequence_to_nef_frame

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/lib/sequence_lib.py”, line 11, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.rpf *********************************************************

plugin nef_pipelines.transcoders.rpf

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/rpf/init.py”, line 17, in

import nef_pipelines.transcoders.rpf.exporters.shifts  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/rpf/exporters/shifts.py”, line 7, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.shifty *********************************************************

plugin nef_pipelines.transcoders.shifty

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/shifty/init.py”, line 23, in

import nef_pipelines.transcoders.shifty.exporters.shifts  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/shifty/exporters/shifts.py”, line 7, in

from pynmrstar import Entry, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.sparky *********************************************************

plugin nef_pipelines.transcoders.sparky

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/sparky/init.py”, line 22, in

import nef_pipelines.transcoders.sparky.exporters.peaks  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/sparky/exporters/peaks.py”, line 10, in

from pynmrstar import Entry, Loop

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************** error in nef_pipelines.transcoders.nmrstar **********************************************************

plugin nef_pipelines.transcoders.nmrstar

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/nmrstar/init.py”, line 22, in

import nef_pipelines.transcoders.nmrstar.importers.project  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/nmrstar/importers/project.py”, line 10, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.talos **********************************************************

plugin nef_pipelines.transcoders.talos

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/talos/init.py”, line 26, in

import nef_pipelines.transcoders.talos.exporters.shifts  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/talos/exporters/shifts.py”, line 14, in

from pynmrstar import Entry

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

******************************************************* error in nef_pipelines.transcoders.xcamshift *********************************************************

plugin nef_pipelines.transcoders.xcamshift

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/xcamshift/init.py”, line 23, in

import nef_pipelines.transcoders.xcamshift.exporters.shifts  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/xcamshift/exporters/shifts.py”, line 6, in

from pynmrstar import Entry, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

****************************************************** error in nef_pipelines.transcoders.xeasy *********************************************************

plugin nef_pipelines.transcoders.xeasy

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/xeasy/init.py”, line 21, in

import nef_pipelines.transcoders.xeasy.importers.peaks  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/xeasy/importers/peaks.py”, line 7, in

from nef_pipelines.lib.nef_lib import (

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/lib/nef_lib.py”, line 11, in

from pynmrstar import Entry, Loop, Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

****************************************************** error in nef_pipelines.transcoders.xplor ********************************************************

plugin nef_pipelines.transcoders.xplor

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 18, in

import pynmrstar.cnmrstar as cnmrstar

ModuleNotFoundError: No module named ‘pynmrstar.cnmrstar’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/main.py”, line 112, in main

import_module(module_name)

File “/usr/lib/python3.10/importlib/init.py”, line 126, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File “”, line 1050, in _gcd_import

File “”, line 1027, in _find_and_load

File “”, line 1006, in _find_and_load_unlocked

File “”, line 688, in _load_unlocked

File “”, line 883, in exec_module

File “”, line 241, in _call_with_frames_removed

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/xplor/init.py”, line 30, in

import nef_pipelines.transcoders.xplor.exporters.rdcs  # noqa: F401

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/nef_pipelines/transcoders/xplor/exporters/rdcs.py”, line 7, in

from pynmrstar import Saveframe

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 23, in

raise ImportError('Could not import cnmrstar sub-module! Your installation appears to be broken.')

ImportError: Could not import cnmrstar sub-module! Your installation appears to be broken.

        WARNING: the following plugins failed to load:



            nef_pipelines.tools.about

nef_pipelines.tools.chains

nef_pipelines.tools.entry

nef_pipelines.tools.fit

nef_pipelines.tools.frames

nef_pipelines.tools.header

nef_pipelines.tools.peaks

nef_pipelines.tools.save

nef_pipelines.tools.series

nef_pipelines.tools.shifts

nef_pipelines.tools.simulate

nef_pipelines.tools.test

nef_pipelines.transcoders.csv

nef_pipelines.transcoders.echidna

nef_pipelines.transcoders.fasta

nef_pipelines.transcoders.mars

nef_pipelines.transcoders.nmrpipe

nef_pipelines.transcoders.nmrview

nef_pipelines.transcoders.pales

nef_pipelines.transcoders.rcsb

nef_pipelines.transcoders.rpf

nef_pipelines.transcoders.shifty

nef_pipelines.transcoders.sparky

nef_pipelines.transcoders.nmrstar

nef_pipelines.transcoders.talos

nef_pipelines.transcoders.xcamshift

nef_pipelines.transcoders.xeasy

nef_pipelines.transcoders.xplor

        the remaining plugins will work but NEF-Pipelines is working  with reduced capabilities. The modules

        that failed to load and the causes of the problem are listed above please report this to the authors

        at github: https://github.com/varioustoxins/NEF-Pipelines/issues

varioustoxins · 12 June 2024 20:39

I know the answer to this one hopefully, you need to do

pipx uninstall nef-pipelines
pipx interpreter -v list

this will give you something like

pipx >(setup:924): pipx version is 1.5.0
pipx >(setup:925): Default python interpreter is ‘PYTHON-INTERPRETER-PATH/python’
Standalone interpreters are in /Users/garyt/Library/Application Support/pipx/py

wherePYTHON-INTERPRETER-PATH is the path to your python interpreter, in my case /Users/garyt/miniconda3/bin

then run

run PYTHON-INTERPRETER-PATH/pipx install --upgrade wheel setuptools
pipx install nef-pipelines

just out of interest what does PYTHON-INTERPRETER-PATH/python --version give you?

explanation some older versions of the pip package installer don’t install the library pynmrstar properly and you need to upgrade the package manager before you can install this library… this seems too be a problem on older linux versions such as centos 7 and ubuntu 22LTS I will add some blurb to the program and website to help clear this up…

Hopefully this fixes things!

regards
Gary

Marta · 13 June 2024 08:30

Hi Gary,
I tried to type

pipx uninstall nef-pipelines
pipx interpreter -v list

The first one works ( stars appear after the command), but the second one give me

usage: pipx [-h] [–version]

        {install,inject,upgrade,upgrade-all,uninstall,uninstall-all,reinstall,reinstall-all,list,run,runpip,ensurepath,completions}

        ...

pipx: error: argument command: invalid choice: ‘interpreter’ (choose from ‘install’, ‘inject’, ‘upgrade’, ‘upgrade-all’, ‘uninstall’, ‘uninstall-all’, ‘reinstall’, ‘reinstall-all’, ‘list’, ‘run’, ‘runpip’, ‘ensurepath’, ‘completions’)

I will try this afternoon with a colleague who is more computer literate than I am. Maybe I am making a mistake in some of the steps.

I will let you know if we can solve the problem.
thanks
Marta :)