Closed michael-liem closed 1 year ago
wdecoster
commented
2 years ago I am a little confused why you are installing things both with conda and pip. I would recommend you stick to one of those installation methods.
The error you report is a duplicate of https://github.com/wdecoster/NanoPlot/issues/201 Please downgrade seaborn to version 0.10.1
michael-liem
commented
2 years ago Why I setup the environment with conda and then inside the environment I install NanoPlot with pip instead of conda you mean?
That is another fix since conda install nanoplot couldn't find the correct channel, even though I run conda config before installing NanoPlot : conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda install nanoplot
It was an - all roads lead to Rome - idea
However, I just retried the conda install nanoplot and now the correct channels are found (apparently), hmmm maybe the datarepo was temporarily unavailable or something . Sorry for the confusing message.
I made another environment using the yml file shown above. Inside the environment I run conda config (as shown above) and then conda install nanoplot, the correct channels are found and the installation is complete.
When I run: NanoPlot -t 10 --fastq reads.fastq --maxlength 40000 --plots dot --legacy hex
I still get this error message:
If you read this then NanoPlot 1.39.0 has crashed :-( Please try updating NanoPlot and see if that helps...
If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues If you could include the log file that would be really helpful. Thanks!
Traceback (most recent call last): File "/home/michael/miniconda3/envs/test2/lib/python3.8/site-packages/nanoplotter/nanoplotter_main.py", line 201, in scatter_legacy import seaborn as sns ModuleNotFoundError: No module named 'seaborn'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/michael/miniconda3/envs/test2/bin/NanoPlot", line 10, in
When I try to update nanoplot with: conda update nanoplot
everything seems up to date according to: Collecting package metadata (current_repodata.json): done Solving environment: done
All requested packages already installed.
Then I rerun the command: NanoPlot -t 10 --fastq reads.fastq --maxlength 40000 --plots dot --legacy hex
and the same error message occurs, it seems that seaborn and matplotlib are not automatically installed when using either pip or conda install?
Do I need to install those manually?
Thank you!
Michael
michael-liem
commented
2 years ago I have figured this out for you; when I make two identical conda environments using a yml file
name: test1 dependencies: -python=3.8
name: test2 dependencies: -python=3.8
Then when I go inside the environments and try to install NanoPlot in two ways: env test1) conda install -c bioconda nanoplot env test2) conda install nanoplot
only the second install is able to finish.
conda install -c bioconda nanoplot is trying to solve the environment but seems to be stuck (its has been trying to solve it for over 30 minutes and is still running)
conda install -c bioconda nanoplot Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: \
It is because of this behavior that I initially decided to install NanoPlot with pip. However due to some coincidental mistake I forgot to indicate the -c bioconda channel during another installation try, to find out NanoPlot actually gets installed when omitting the -c flag during installation.
I created an conda environment with the following nanoplot.yml file:
name: nanoplot dependencies: -python=3.8
create environment $conda env create --file nanoplot.yml $conda activate nanoplot
install and upgrade nanoplot $pip install NanoPlot $pip install NanoPlot --upgrade
hereafter I got an error message indicating matplotlib and seaborn was not installed, I tried to fix it with: $python -m pip install --user matplotlib seaborn
at this point I do get a plot (yeah) but there are still error messages showing up: NanoPlot -t 10 --fastq ~/file.fastq --maxlength 40000 --plots dot --legacy hex
If you read this then NanoPlot 1.39.0 has crashed :-( Please try updating NanoPlot and see if that helps...
If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues If you could include the log file that would be really helpful. Thanks!
Traceback (most recent call last): File "/home/michael/miniconda3/envs/daur2/bin/NanoPlot", line 8, in
sys.exit(main())
File "/home/michael/miniconda3/envs/daur2/lib/python3.8/site-packages/nanoplot/NanoPlot.py", line 109, in main
plots = make_plots(datadf, settings)
File "/home/michael/miniconda3/envs/daur2/lib/python3.8/site-packages/nanoplot/NanoPlot.py", line 181, in make_plots
nanoplotter.scatter(
File "/home/michael/miniconda3/envs/daur2/lib/python3.8/site-packages/nanoplotter/nanoplotter_main.py", line 172, in scatter
plots_made += scatter_legacy(x=x[idx],
File "/home/michael/miniconda3/envs/daur2/lib/python3.8/site-packages/nanoplotter/nanoplotter_main.py", line 231, in scatter_legacy
plot = sns.jointplot(
File "/home/michael/miniconda3/envs/daur2/lib/python3.8/site-packages/seaborn/_decorators.py", line 46, in inner_f
return f(kwargs)
File "/home/michael/miniconda3/envs/daur2/lib/python3.8/site-packages/seaborn/axisgrid.py", line 2300, in jointplot
grid.plot_joint(plt.hexbin, joint_kws)
File "/home/michael/miniconda3/envs/daur2/lib/python3.8/site-packages/seaborn/axisgrid.py", line 1808, in plot_joint
func(self.x, self.y, *kwargs)
File "/home/michael/.local/lib/python3.8/site-packages/matplotlib/pyplot.py", line 2572, in hexbin
ret = gca().hexbin(
File "/home/michael/.local/lib/python3.8/site-packages/matplotlib/init__.py", line 1412, in inner
return func(ax, map(sanitize_sequence, args), **kwargs)
File "/home/michael/.local/lib/python3.8/site-packages/matplotlib/axes/_axes.py", line 4824, in hexbin
collection.update(kwargs)
File "/home/michael/.local/lib/python3.8/site-packages/matplotlib/artist.py", line 1064, in update
raise AttributeError(f"{type(self).name!r} object "
AttributeError: 'PolyCollection' object has no property 'stat_func'
Hope this helps to improve,
Cheers, Michael
p.s. I just figured out then when I omit the flag --legacy hex no error messages occur