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UserWarning: Warning: representative contig wasn't circularized #87

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Qikiiso opened this issue Apr 7, 2024 · 0 comments
Open

UserWarning: Warning: representative contig wasn't circularized #87

Qikiiso opened this issue Apr 7, 2024 · 0 comments

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@Qikiiso
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Qikiiso commented Apr 7, 2024

Hello, I am getting the following error when running the tool on a plant sample.
I don't see any prior reference to this and was wondering if you have any advice on how to proceed.

2024-04-04 02:39:10 [INFO] 10. Building annotation plots for all contigs
/disk1/xsq/software/MitoHiFi/src/getReprContig.py:197: UserWarning: Warning: representative contig wasn't circularized
repr_contig_id, repr_contig_cluster = get_repr_contig_info(cdhit_out_clstr, rel_mito_len, rel_mito_num_genes, debug=debug)
Traceback (most recent call last):
File "/disk1/xsq/software/MitoHiFi/src/mitohifi.py", line 565, in
main()
File "/disk1/xsq/software/MitoHiFi/src/mitohifi.py", line 490, in main
plot_annotation.plot_annotation("final_mitogenome.gb", "final_mitogenome.annotation.png")
File "/disk1/xsq/software/MitoHiFi/src/plot_annotation.py", line 39, in plot_annotation
ax, _ = graphic_record.plot(figure_width=10, strand_in_label_threshold=7)
File "/home/xsq/miniconda3/envs/mitohifi_env/lib/python3.7/site-packages/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py", line 438, in plot
fig, ax = plt.subplots(1, figsize=(figure_width, height))
File "/home/xsq/miniconda3/envs/mitohifi_env/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1177, in subplots
fig = figure(**fig_kw)
File "/home/xsq/miniconda3/envs/mitohifi_env/lib/python3.7/site-packages/matplotlib/pyplot.py", line 546, in figure
**kwargs)
File "/home/xsq/miniconda3/envs/mitohifi_env/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 3358, in new_figure_manager
return cls.new_figure_manager_given_figure(num, fig)
File "/home/xsq/miniconda3/envs/mitohifi_env/lib/python3.7/site-packages/matplotlib/backends/_backend_tk.py", line 888, in new_figure_manager_given_figure
window = tk.Tk(className="matplotlib")
File "/home/xsq/miniconda3/envs/mitohifi_env/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:10.0"

I'm running the following command:

nohup python /disk1/xsq/software/MitoHiFi/src/mitohifi.py -r YTJ.ccs.fastq.gz -f B.variegata-mitochondrion.fasta -g sequence.gb -t 36 -a plant -o 1

Can you help me resolve this issue?

Good luck!

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