Open kapsakcj opened 4 years ago
I don't get this error when running the container with docker, nor do I see this issue on pulsestar2 with docker or singularity (3.5.3). I think it's specific to the monolith computers
It's important to include the -C
flag when running socru with singularity on the monoliths. (still need to test on aspen/HPC)
-C|--containall Contain not only file systems, but also PID, IPC, and environment
If not, socru will throw X11 errors:
# this works
$ ml singularity/2.6.1
$ singularity shell -C --no-home -B $PWD:/data ~/singularity-images/socru.2.2.4.simg
$ socru Escherichia_coli barcode01/medaka/consensus.fasta
barcode01/medaka/consensus.fasta GREEN GS1.0 1 2 3 4 5 6 7
# this throws errors (using same singularity 2.6.1 module)
$ singularity shell --no-home -B $PWD:/data ~/singularity-images/socru.2.2.4.simg
$ socru Escherichia_coli barcode01/medaka/consensus.fasta
X11 connection rejected because of wrong authentication.
X11 connection rejected because of wrong authentication.
Traceback (most recent call last):
File "/opt/conda/bin/socru", line 69, in <module>
g.run()
File "/opt/conda/lib/python3.7/site-packages/socru/Socru.py", line 68, in run
output_type = self.run_analysis(i, p, d)
File "/opt/conda/lib/python3.7/site-packages/socru/Socru.py", line 183, in run_analysis
pp.create_plot()
File "/opt/conda/lib/python3.7/site-packages/socru/PlotProfile.py", line 26, in create_plot
piechart = plt.pie(size, labels=names, wedgeprops = { 'linewidth' : 7, 'edgecolor' : 'white' })
File "/opt/conda/lib/python3.7/site-packages/matplotlib/pyplot.py", line 2781, in pie
return gca().pie(
File "/opt/conda/lib/python3.7/site-packages/matplotlib/pyplot.py", line 926, in gca
return gcf().gca(**kwargs)
File "/opt/conda/lib/python3.7/site-packages/matplotlib/pyplot.py", line 610, in gcf
return figure()
File "/opt/conda/lib/python3.7/site-packages/matplotlib/pyplot.py", line 545, in figure
**kwargs)
File "/opt/conda/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 3261, in new_figure_manager
return cls.new_figure_manager_given_figure(num, fig)
File "/opt/conda/lib/python3.7/site-packages/matplotlib/backends/_backend_tk.py", line 950, in new_figure_manager_given_figure
window = tk.Tk(className="matplotlib")
File "/opt/conda/lib/python3.7/tkinter/__init__.py", line 2023, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: couldn't connect to display "localhost:12.0"
^ This occurred when using the docker image provided by Andrew at docker://quadraminstitute/socru:version-2.2.4
built using singularity 2.6.1 with singularity build socru.2.2.4.simg docker://quadraminstitute/socru:version-2.2.4
socru is not yet in StaPH-B/docker-builds, but I may make my own dockerfile and add it, if that would mean I could avoid these X11 errors
Will be useful for assessing the quality of complete, circularized assemblies and identifying mis-assemblies.
Will be species specific, and user will need to input the species.
socru has a long list of available/supported species which includes: