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Hi, I got a problem when run run_test.sh, see below.
Starting VCF files analysis... Step 1: Extract results for mirnaome Cleaning output folder checking: input_files/input_vcf/example_vcf_set/sample01.vcf checking: input_files/input_vcf/example_vcf_set/sample03.vcf checking: input_files/input_vcf/example_vcf_set/sample02.vcf 1 / 3 input_files/input_vcf/example_vcf_set/sample01.vcf 2 / 3 input_files/input_vcf/example_vcf_set/sample03.vcf 3 / 3 input_files/input_vcf/example_vcf_set/sample02.vcf Step 2 (optional): Merge all algorithms and filter mutations Step 3: Add miRNA information Step 4: Add mutation weights and HGVS nomenclature Step 5: Make complex, distinct and occure files Step 6: All mutations visualizations Traceback (most recent call last): File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/run_mirnaome_analysis.py", line 104, in main() File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 1130, in call return self.main(*args, **kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/run_mirnaome_analysis.py", line 95, in main prepare_figure(output_folder) File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/mutation_loc_figures.py", line 445, in prepare_figure create_plot(df_temp, output_folder + '/plots/plot_miRNA.svg', File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/mutation_loc_figures.py", line 144, in create_plot plt.grid(b=True, which='major', axis='y', color='lightgrey', File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/pyplot.py", line 2616, in grid return gca().grid(visible=visible, which=which, axis=axis, **kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 3196, in grid self.yaxis.grid(visible, which=which, **kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axis.py", line 1660, in grid self.set_tick_params(which='major', **gridkw) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axis.py", line 932, in set_tick_params kwtrans = self._translate_tick_params(kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axis.py", line 1076, in _translate_tick_params raise ValueError( ValueError: keyword grid_b is not recognized; valid keywords are ['size', 'width', 'color', 'tickdir', 'pad', 'labelsize', 'labelcolor', 'zorder', 'gridOn', 'tick1On', 'tick2On', 'label1On', 'label2On', 'length', 'direction', 'left', 'bottom', 'right', 'top', 'labelleft', 'labelbottom', 'labelright', 'labeltop', 'labelrotation', 'grid_agg_filter', 'grid_alpha', 'grid_animated', 'grid_antialiased', 'grid_clip_box', 'grid_clip_on', 'grid_clip_path', 'grid_color', 'grid_dash_capstyle', 'grid_dash_joinstyle', 'grid_dashes', 'grid_data', 'grid_drawstyle', 'grid_figure', 'grid_fillstyle', 'grid_gapcolor', 'grid_gid', 'grid_in_layout', 'grid_label', 'grid_linestyle', 'grid_linewidth', 'grid_marker', 'grid_markeredgecolor', 'grid_markeredgewidth', 'grid_markerfacecolor', 'grid_markerfacecoloralt', 'grid_markersize', 'grid_markevery', 'grid_mouseover', 'grid_path_effects', 'grid_picker', 'grid_pickradius', 'grid_rasterized', 'grid_sketch_params', 'grid_snap', 'grid_solid_capstyle', 'grid_solid_joinstyle', 'grid_transform', 'grid_url', 'grid_visible', 'grid_xdata', 'grid_ydata', 'grid_zorder', 'grid_aa', 'grid_c', 'grid_ds', 'grid_ls', 'grid_lw', 'grid_mec', 'grid_mew', 'grid_mfc', 'grid_mfcalt', 'grid_ms']
Starting VCF files analysis...
Step 1: Extract results for mirnaome Cleaning output folder checking: input_files/input_vcf/example_vcf_set/sample01.vcf checking: input_files/input_vcf/example_vcf_set/sample03.vcf checking: input_files/input_vcf/example_vcf_set/sample02.vcf 1 / 3
input_files/input_vcf/example_vcf_set/sample01.vcf 2 / 3
input_files/input_vcf/example_vcf_set/sample03.vcf 3 / 3
input_files/input_vcf/example_vcf_set/sample02.vcf Step 2 (optional): Merge all algorithms and filter mutations Step 3: Add miRNA information Step 4: Add mutation weights and HGVS nomenclature Step 5: Make complex, distinct and occure files Step 6: All mutations visualizations Traceback (most recent call last): File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/run_mirnaome_analysis.py", line 104, in main() File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 1130, in call return self.main(*args, **kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/run_mirnaome_analysis.py", line 95, in main prepare_figure(output_folder) File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/mutation_loc_figures.py", line 445, in prepare_figure create_plot(df_temp, output_folder + '/plots/plot_miRNA.svg', File "/Users/wenqingfeng/Desktop/multi_omics_AD/CSV/mirnome-mutations/mutation_loc_figures.py", line 144, in create_plot plt.grid(b=True, which='major', axis='y', color='lightgrey', File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/pyplot.py", line 2616, in grid return gca().grid(visible=visible, which=which, axis=axis, **kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 3196, in grid self.yaxis.grid(visible, which=which, **kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axis.py", line 1660, in grid self.set_tick_params(which='major', **gridkw) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axis.py", line 932, in set_tick_params kwtrans = self._translate_tick_params(kwargs) File "/Users/wenqingfeng/miniconda3/lib/python3.10/site-packages/matplotlib/axis.py", line 1076, in _translate_tick_params raise ValueError( ValueError: keyword grid_b is not recognized; valid keywords are ['size', 'width', 'color', 'tickdir', 'pad', 'labelsize', 'labelcolor', 'zorder', 'gridOn', 'tick1On', 'tick2On', 'label1On', 'label2On', 'length', 'direction', 'left', 'bottom', 'right', 'top', 'labelleft', 'labelbottom', 'labelright', 'labeltop', 'labelrotation', 'grid_agg_filter', 'grid_alpha', 'grid_animated', 'grid_antialiased', 'grid_clip_box', 'grid_clip_on', 'grid_clip_path', 'grid_color', 'grid_dash_capstyle', 'grid_dash_joinstyle', 'grid_dashes', 'grid_data', 'grid_drawstyle', 'grid_figure', 'grid_fillstyle', 'grid_gapcolor', 'grid_gid', 'grid_in_layout', 'grid_label', 'grid_linestyle', 'grid_linewidth', 'grid_marker', 'grid_markeredgecolor', 'grid_markeredgewidth', 'grid_markerfacecolor', 'grid_markerfacecoloralt', 'grid_markersize', 'grid_markevery', 'grid_mouseover', 'grid_path_effects', 'grid_picker', 'grid_pickradius', 'grid_rasterized', 'grid_sketch_params', 'grid_snap', 'grid_solid_capstyle', 'grid_solid_joinstyle', 'grid_transform', 'grid_url', 'grid_visible', 'grid_xdata', 'grid_ydata', 'grid_zorder', 'grid_aa', 'grid_c', 'grid_ds', 'grid_ls', 'grid_lw', 'grid_mec', 'grid_mew', 'grid_mfc', 'grid_mfcalt', 'grid_ms']
I've got all packages installed successfully, just wonder how I can solve this? Many thanks!
Best, Wen
The text was updated successfully, but these errors were encountered:
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Hi, I got a problem when run run_test.sh, see below.
I've got all packages installed successfully, just wonder how I can solve this? Many thanks!
Best,
Wen
The text was updated successfully, but these errors were encountered: