Error creating Krona plots in metaquast.py

[RayanaFeltrin]

Hello!

I have recently run the command metaquast.py -o quast_ANT001 --large -l metaSPAdes,MEGAHIT meta_assembly_001ANT/contigs.fasta mega_assembly_001ANT/final.contigs.fa

At the final step of the software, I got the following error, which was also obtained in #216, #246 and #237 and still not solved:

Drawing interactive Krona plots...

'NoneType' object is not iterable
Traceback (most recent call last):
File "/home/rayana/Desktop/tools/quast/metaquast.py", line 427, in
return_code = main(sys.argv[1:])
File "/home/rayana/Desktop/tools/quast/metaquast.py", line 417, in main
html_saver.create_meta_report(output_dirpath, json_texts)
File "/home/rayana/Desktop/tools/quast/quast_libs/html_saver/html_saver.py", line 257, in create_meta_report
create_krona_charts(taxons_for_krona, meta_log, results_dirpath, json_texts)
File "/home/rayana/Desktop/tools/quast/quast_libs/html_saver/html_saver.py", line 363, in create_krona_charts
for section in report:
TypeError: 'NoneType' object is not iterable

I have also tried to install Krona separately and put ~/Desktop/tools/Krona/KronaTools in the ~/.bashrc file, but nothing has changed.

I really need to solve this to continue my work and would appreciate any help.

Thank you in advance.

[RayanaFeltrin]

@alexeigurevich @vyahhi @asl @ad3002 @sjackman, help please!

[alexeigurevich]

@RayanaFeltrin sorry for the huge delay, I am looking into this right now!

[alexeigurevich]

I just submitted a dirty workaround to the master branch. You can now run metaquast.py with the --no-krona option to skip the creation of Krona charts. In this case, at least everything else will be completed and you will have all other MetaQUAST reports including interactive HTML files.

I am still looking into this issue and hopefully will have a proper fix soon, so the Krona charts will be created when possible.
After that, I plan to prepare a bugfix release 5.2.1 and will close this and three related issues.

[RayanaFeltrin]

Thank you, @alexeigurevich ! I've just runned it with --no-krona and got to open the HTML file.

[bheimbu]

Hi @alexeigurevich,

any news about this issue? I'm encountering the same problem. Actually, I'd like to use quast installed with mamba, but this comes without --no-krona option resulting in a failed run.

Cheers Bastian

[RayanaFeltrin]

Hello @alexeigurevich!

I am also facing the same problem as @bheimbu... I've run the following command in a Slurm cluster:
metaquast.py scaffolds.fasta final.contigs.fa -o quast_ANT001 -t 10 --large --no-krona > quast_ANT001.out 2> quast_ANT001.err

... and got the error:

Usage: metaquast.py [options]

metaquast.py: error: no such option: --no-krona

What could I do to solve this?
Thank you in advance!

[bgruening]

@alexeigurevich can you please create a new release? I can create a new conda package.

[LottePronk]

I'm encountering the same error and I need the conda package to integrate into a pipeline. Any idea when a new release will be coming?

[alexeigurevich]

The feature is finally released in v.5.3.0 today! Furthermore, we automatically catch the error and prevent the crash, so there is no need to specify explicitly --no-krona (but you can still do it).

@bgruening, could you please update on conda when you have time?

[bgruening]

Yes, I can take care of this. Thanks for fixing.

[bgruening]

The Conda package and the Containers are up, the Galaxy integrations will come tomorrow.

I saw this here in the logs:

Python recognizes 'quast_libs.minimap2.sse2neon' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
 
 This leads to an ambiguous overall configuration. If you want to distribute this
 package, please make sure that 'quast_libs.minimap2.sse2neon' is explicitly added
 to the `packages` configuration field.

Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" on setuptools documentation page:
 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

[RayanaFeltrin]

Thank you so much @alexeigurevich @bgruening!

Best