gbouras13
commented
2 months ago Hi @JEMINA-JOHN ,
I think the issue is the phold output - there are some differences in how pharokka handles it.
I would simply recommend using phold plot e.g.
phold plot -i /content/output_phold/phold.gbk -o pharokka_plots_output_directory
This by default will plot each entry in the Genbank separately (like pharokka_multiplotter.py)
George
Description
I was trying to use multiplotter to plot the output of pharokka and phold. In run_pharokka_and_phold.ipynb, i got output from pharokka and phold. I wanted to plot phold output using multiplotter but keep getting this error. I am new to coding so I am not able to understand what exactly is the issue. I am able to understand the fact that its because of the .gbk file. But that was generated by pharokka and phold only. So i am not sure why the structure of file will create an issue.
Am i doing anything wrong? Can someone help? @gbouras13
What I Did
!pharokka_multiplotter.py -g /content/output_phold/phold.gbk -o pharokka_plots_output_directory
2024-04-11 15:15:37.250 | INFO | main::103 - Starting Pharokka v1.7.1
2024-04-11 15:15:37.250 | INFO | main::104 - Running pharokka_multiplotter.py to plot your phages.
2024-04-11 15:15:37.250 | INFO | main::105 - Command executed: Namespace(genbank='/content/output_phold/phold.gbk', outdir='pharokka_plots_output_directory', force=False, label_hypotheticals=False, remove_other_features_labels=False, title_size='20', label_size='8', interval='5000', truncate='20', dpi='600', annotations='1', plot_title='Phage', label_ids='')
2024-04-11 15:15:37.250 | INFO | main::106 - Repository homepage is https://github.com/gbouras13/pharokka
2024-04-11 15:15:37.250 | INFO | main::107 - Written by George Bouras: george.bouras@adelaide.edu.au
2024-04-11 15:15:37.250 | INFO | main::108 - Checking your inputs.
2024-04-11 15:15:37.251 | INFO | main::194 - All files checked.
2024-04-11 15:15:37.285 | INFO | main::244 - Plotting NODE_10_length_1884_cov_1.569
Traceback (most recent call last):
File "/usr/local/bin/pharokka_multiplotter.py", line 246, in
create_single_plot(
File "/usr/local/bin/plot.py", line 970, in create_single_plot
quantile_length = np.quantile(length_list, annotations)
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4543, in quantile
return _quantile_unchecked(
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4555, in _quantile_unchecked
return _ureduce(a,
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 3823, in _ureduce
r = func(a, **kwargs)
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4722, in _quantile_ureduce_func
result = _quantile(arr,
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4831, in _quantile
slices_having_nans = np.isnan(arr[-1, ...])
IndexError: index -1 is out of bounds for axis 0 with size 0
output_phold.zip output_pharokka.zip
The gbk file inside these outputs only i used. I unzipped the file and ran the gbk file only. Cannot figure where the issue is.