Closed Fatihlrcfs closed 2 years ago
wdecoster
commented
2 years ago Hi,
That has been reported before, e.g. https://github.com/wdecoster/NanoPlot/issues/201 I think if you update NanoPlot (or downgrade seaborn to v0.10.1) you should be fine.
Cheers, Wouter
Fatihlrcfs
commented
2 years ago Hi Wouter,
thank you for your response. I update Nanoplot (this time second example command =NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots dot))but ı am still getting error. like below. could you offer me any other options. many thanks
Sincerely,
/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/distributions.py:2619: FutureWarning: distplot is a deprecated function and will be removed in a future version. Please adapt your code to use either displot (a figure-level function with similar flexibility) or histplot (an axes-level function for histograms).
warnings.warn(msg, FutureWarning)
Traceback (most recent call last):
File "/cluster/lrcfs/ftiras/ftiras_env/bin/NanoPlot", line 10, in
wdecoster
commented
2 years ago Can you please post the output of NanoPlot --version. The current version is 1.38.1
Fatihlrcfs
commented
2 years ago hi Wouter,
mine say 1.32.1 :( ı updated all packages today. and when ı tried to update or install again its says = All requested packages already installed). is there a special command for the update of the NanoPlot? I am so sorry for this problem. but many thanks for your help.
Kind Regards.
wdecoster
commented
2 years ago Then it seems your update command did not actually lead to an update. Are you installing with conda or pip? Or perhaps there is still an older installation elsewhere on your system which takes precedence.
Fatihlrcfs
commented
2 years ago Conda and ı used conda install NanoPlot and update command. thanks
wdecoster
commented
2 years ago Could you maybe try pip uninstall NanoPlot and see if that changes the version you get?
Fatihlrcfs
commented
2 years ago Successfully uninstalled NanoPlot-1.32.1. Now can ı install again now using conda install NanoPlot command When ı tried to install again it said # All requested packages already installed.
wdecoster
commented
2 years ago Okay, and what is the version now?
Fatihlrcfs
commented
2 years ago the problem is still saying # All requested packages already installed. but there is no packages or files and says NanoPlot: command not found. Also, I checked the files virtually and there are no files for NanoPlot. Thanks
Hi Dear,
I got an error during the Nanoplot run and it was crashed. I copied what was present on my screen and log file also. thanks
(base) [2397405@login1 data]$ cd /cluster/lrcfs/ftiras/projects/nanopore_testing/data/First\ run\ 61\ years\ male/basecalledmodbase5mchac28x2/ (base) [2397405@login1 basecalledmodbase5mchac28x2]$ NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed /cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/_collections_abc.py:702: MatplotlibDeprecationWarning: The global colormaps dictionary is no longer considered public API. return len(self._mapping) /cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/_collections_abc.py:720: MatplotlibDeprecationWarning: The global colormaps dictionary is no longer considered public API. yield from self._mapping /cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/distributions.py:2557: FutureWarning:
distplotis a deprecated function and will be removed in a future version. Please adapt your code to use eitherdisplot(a figure-level function with similar flexibility) orhistplot(an axes-level function for histograms). warnings.warn(msg, FutureWarning)If you read this then NanoPlot 1.32.1 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 "/cluster/lrcfs/ftiras/ftiras_env/bin/NanoPlot", line 10, in
sys.exit(main())
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/nanoplot/NanoPlot.py", line 101, in main
plots = make_plots(datadf, settings)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/nanoplot/NanoPlot.py", line 160, in make_plots
nanoplotter.scatter(
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/nanoplotter/nanoplotter_main.py", line 159, in scatter
plot = sns.jointplot(
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/_decorators.py", line 46, in inner_f
return f(kwargs)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/axisgrid.py", line 2135, in jointplot
grid.plot_joint(scatterplot, joint_kws)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/axisgrid.py", line 1734, in plot_joint
func(x=self.x, y=self.y, kwargs)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/_decorators.py", line 46, in inner_f
return f(kwargs)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/relational.py", line 820, in scatterplot
p.plot(ax, kwargs)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/seaborn/relational.py", line 608, in plot
scout = ax.scatter(scout_x, scout_y, *kws)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/matplotlib/init.py", line 1361, in inner
return func(ax, map(sanitize_sequence, args), **kwargs)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/matplotlib/axes/_axes.py", line 4597, in scatter
collection.update(kwargs)
File "/cluster/lrcfs/ftiras/ftiras_env/lib/python3.8/site-packages/matplotlib/artist.py", line 1062, in update
raise AttributeError(f"{type(self).name!r} object "
AttributeError: 'PathCollection' object has no property 'stat_func'
(base) [2397405@login1 basecalledmodbase5mchac28x2]$
Broadcast message from root@login1.compute.dundee.ac.uk (Mon 2021-10-18 17:00:00 BST):
Rebooting for system updates The system is going down for reboot at Tue 2021-10-19 08:00:00 BST!
NanoPlot_20211018_1655.log