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Issue with MAG_DEPTHS_PLOT
I'm running mag in my institution's cluster and in the MAG_DEPTHS_PLOT step I run into the error _tkinter.TclError: couldn't connect to display "localhost:11.0".
For what I've read, I guess that's some issue related to X11. When I connect to the cluster via ssh I allow X11 since I have this written in my .ssh/config:
Host *
ForwardAgent yes
ForwardX11 yes
Do I need to start a X11 session before running the pipeline? But I can't since I'm not root of the cluster. What seems easiest for me is to skip this process in the pipeline, but I don't see any flag to do it and it's a required process for the pipeline to continue. Any ideas of what can I do or whether this skip flag could be added to the pipeline?
Here's the full error message:
Error executing process > 'NFCORE_MAG:MAG:BINNING:MAG_DEPTHS_PLOT (SPAdes-MaxBin2-test_minigut)'
Caused by:
Process `NFCORE_MAG:MAG:BINNING:MAG_DEPTHS_PLOT (SPAdes-MaxBin2-test_minigut)` terminated with an error exit status (1)
Command executed:
plot_mag_depths.py --bin_depths SPAdes-MaxBin2-test_minigut-binDepths.tsv --groups sample_groups.tsv
--out "SPAdes-MaxBin2-test_minigut-binDepths.heatmap.png"
cat <<-END_VERSIONS > versions.yml
"NFCORE_MAG:MAG:BINNING:MAG_DEPTHS_PLOT":
python: $(python --version 2>&1 | sed 's/Python //g')
pandas: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)")
seaborn: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('seaborn').version)")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/home/xrey/.nextflow/assets/nf-core/mag/bin/plot_mag_depths.py", line 71, in <module>
sys.exit(main())
File "/home/xrey/.nextflow/assets/nf-core/mag/bin/plot_mag_depths.py", line 54, in main
plt.figure()
File "/home/xrey/miniconda3/envs/nf_mag/lib/python3.6/site-packages/matplotlib/pyplot.py", line 693, in figure
**kwargs)
File "/home/xrey/miniconda3/envs/nf_mag/lib/python3.6/site-packages/matplotlib/pyplot.py", line 315, in new_figure_manager
return cls.new_figure_manager_given_figure(num, fig)
File "/home/xrey/miniconda3/envs/nf_mag/lib/python3.6/site-packages/matplotlib/backends/_backend_tk.py", line 885, in new_figure_manager_given_figure
window = tk.Tk(className="matplotlib")
File "/home/xrey/miniconda3/envs/nf_mag/lib/python3.6/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:11.0"
Work dir:
/mnt/lustre/scratch/xrey/genomes/nextflow-mag/work/e7/09028286e27279854f9425097af44e
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line