Open josephhughes opened 3 years ago
mvvucak
commented
3 years ago I'm unable to reproduce this on Alpha with my set-up. Could you tell me what versions of seaborn and matplotlib your environment is using? Also, is this happening on a local machine or while connecting to Alpha remotely?
It looks like Seaborn is setting matplotlib's backend to 'TkAgg' which is interactive and requires ssh -X or ssh -Y to function. Might be a quick fix if that's the issue.
josephhughes
commented
3 years ago This isn't on Alpha. I'm thinking we may need to test weeSAM on more systems or roll-it back to a version with fewer dependencies.
On Mon, Jun 28, 2021 at 5:00 PM mvvucak @.***> wrote:
I'm unable to reproduce this on Alpha with my set-up. Could you tell me what versions of seaborn and matplotlib your environment is using? Also, is this happening on a local machine or while connecting to Alpha remotely?
It looks like Seaborn is setting matplotlib's backend to 'TkAgg' which is interactive and requires ssh -X or ssh -Y to function. Might be a quick fix if that's the issue.
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weeSAM --bam SARS-CoV-2.bam --html SARS1 --overwrite /usr/local/bin/weeSAM:54: UserWarning: This call to matplotlib.use() has no effect because the backend has already been chosen; matplotlib.use() must be called before pylab, matplotlib.pyplot, or matplotlib.backends is imported for the first time. The backend was originally set to 'TkAgg' by the following code: File "/usr/local/bin/weeSAM", line 52, in
import seaborn as sb
File "/opt/miniconda3/lib/python3.7/site-packages/seaborn/init.py", line 2, in
from .rcmod import * # noqa: F401,F403
File "/opt/miniconda3/lib/python3.7/site-packages/seaborn/rcmod.py", line 7, in
from . import palettes
File "/opt/miniconda3/lib/python3.7/site-packages/seaborn/palettes.py", line 9, in
from .utils import desaturate, get_color_cycle
File "/opt/miniconda3/lib/python3.7/site-packages/seaborn/utils.py", line 14, in
import matplotlib.pyplot as plt
File "/opt/miniconda3/lib/python3.7/site-packages/matplotlib/pyplot.py", line 71, in
from matplotlib.backends import pylab_setup
File "/opt/miniconda3/lib/python3.7/site-packages/matplotlib/backends/init.py", line 17, in
line for line in traceback.format_stack()
matplotlib.use('agg')
---- Processing: SARS-CoV-2.bam ----
Total # Mapped Reads: 212313
Total # Unmapped Reads: 0
Total # Reads: 212313
Generating a depth file, this may take a while.
Processing: SARS-CoV-2 ....
Traceback (most recent call last):
File "/usr/local/bin/weeSAM", line 797, in
process_bam(bam_list)
File "/usr/local/bin/weeSAM", line 657, in process_bam
fig = my_plot(min_dict[i], i)
File "/usr/local/bin/weeSAM", line 343, in my_plot
fig = plt.figure(figsize=(16, 6))
File "/opt/miniconda3/lib/python3.7/site-packages/matplotlib/pyplot.py", line 533, in figure
**kwargs)
File "/opt/miniconda3/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 161, in new_figure_manager
return cls.new_figure_manager_given_figure(num, fig)
File "/opt/miniconda3/lib/python3.7/site-packages/matplotlib/backends/_backend_tk.py", line 1046, in new_figure_manager_given_figure
window = Tk.Tk(className="matplotlib")
File "/opt/miniconda3/lib/python3.7/tkinter/init.py", line 2023, in init
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable