MCscan - Attribute error

[trupper01]

i am trying to Run MCscan to do microsynteny analysis. but i encounter this error :
File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/smita/.local/lib/python3.8/site-packages/jcvi/compara/catalog.py", line 982, in
main()
File "/home/smita/.local/lib/python3.8/site-packages/jcvi/compara/catalog.py", line 88, in main
p.dispatch(globals())
File "/home/smita/.local/lib/python3.8/site-packages/jcvi/apps/base.py", line 130, in dispatch
globalsaction
File "/home/smita/.local/lib/python3.8/site-packages/jcvi/compara/catalog.py", line 655, in ortholog
dotplot_group.add_argument(
AttributeError: 'NoneType' object has no attribute 'add_argument'

Any idea why and how to solve it?

Thank you in advance

[tanghaibao]

@trupper01

There was a bug introduced in an earlier version last week. Can you try updating jcvi to the latest version?
pip install -U jcvi should get this fix. Let me know if the issue persists.

[trupper01]

Hello, i have try it and it working well now. Thank you!

[zhaozhaocuicui]

I encountered the same problem, but the method provided above did not solve the problem
Traceback (most recent call last):
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 982, in
main()
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 88, in main
p.dispatch(globals())
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/apps/base.py", line 130, in dispatch
globalsaction
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 768, in ortholog
dotplot_main(dargs)
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/graphics/dotplot.py", line 518, in dotplot_main
dotplot(
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/graphics/dotplot.py", line 352, in dotplot
xlim, _ = plot_breaks_and_labels(
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/graphics/dotplot.py", line 159, in plot_breaks_and_labels
th = TextHandler(fig, usetex=usetex)
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/graphics/base.py", line 93, in init
self.build_height_array(fig, usetex=usetex)
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/graphics/base.py", line 109, in build_height_array
w, h = TextHandler.get_text_width_height(fig, size=i, usetex=usetex)
File "/home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages/jcvi/graphics/base.py", line 101, in get_text_width_height
tp = mpl.textpath.TextPath((0, 0), txt, size=size, u

[zhaozhaocuicui]

@tanghaibao
This is my updated version information：
(JCVI) t030519@stark03-server:~/tobaco/genome/cds$ pip show jcvi
Name: jcvi
Version: 1.4.11
Summary: Python utility libraries on genome assembly, annotation and comparative genomics
Home-page: http://github.com/tanghaibao/jcvi
Author: Haibao Tang, Vivek Krishnakumar, Jingping Li
Author-email: [email protected]
License: BSD
Location: /home/data/t030519/mambaforge-pypy3/envs/JCVI/lib/python3.10/site-packages
Requires: biopython, boto3, brewer2mpl, CrossMap, deap, ete3, ftpretty, genomepy, gffutils, goatools, graphviz, jinja2, matplotlib, more-itertools, natsort, networkx, numpy, ortools, pybedtools, pyefd, pypdf, pytesseract, rich, scikit-image, scipy, seaborn, Wand, webcolors
Required-by:

[zhaozhaocuicui]

@tanghaibao

[tanghaibao]

This is a common latex issue:
#543

[zhaozhaocuicui]

Okay, thank you, but I still have a question. Why does the previous Python script report an error before the LaTeX issue

[tanghaibao]

I guess when doing pip install -U it also upgrades the dependencies (including matplotlib)
This problem is really because the new version of matplotlib requires: matplotlib/matplotlib#16911

[zhaozhaocuicui]

Okay, thank you very much. I'll give it a try