ERROR! exception caught! in QUAST v5.2.0

[ReneKat]

Hello wonderful quast developers,

I am on a Ubuntu 20.04 Linux machine with QUAST v5.2.0 installed.
I'm running metaquast.py on 3 co-assemblies. It looks like it's failing during MetaGeneMark:

...

All references were combined in combined_reference.fasta

Starting quast.py for the combined reference...
(logging to /home/fch/Projects/LG6/02_Assembly/quast/combined_reference/quast.log)

Error sending result: '[([<quast_libs.genes_parser.Gene object at 0x7f3f4773d990>, <quast_libs.genes_parser.Gene object at 0x7f3f4773db10>, <quast
_libs.genes_parser.Gene object at 0x7f3f4773da90>, <quast_libs.genes_parser.Gene object at 0x7f3f4773dc10>, ............ <quast_libs.genes_parser.Gene object at 0x7f3c47e9bd90>, <quast_libs.genes_parser.Gene object at 0x7f3c47e9bd50>, <quast_libs.genes_parser.Gene object at 0x7f3c47e9bdd0>], 3445978, [2729804, 2085118, 197989, 17017], [724152, 518380, 19525, 1328])]'. Reason: 'error("'i' format requires -2147483648 <= number <= 2147483647")'
ERROR! exception caught!

Please let me know what other information you need.
Thanks so much!
Rene

quast.log
metaquast.log.gz

[ReneKat]

Hello again,
I went ahead and ran metaquast.py again but this time without the gene-calling -f argument. However, I got a similar exception caught:

Drawing NGA50 metaQUAST summary plot...
saved to /home/fch/Projects/LG6/02_Assembly/quast/summary/PDF/NGA50.pdf
Drawing LGA50 metaQUAST summary plot...
saved to /home/fch/Projects/LG6/02_Assembly/quast/summary/PDF/LGA50.pdf

Text versions of reports and plots for each metric (for all references and assemblies) are saved to /home/fch/Projects/LG6/02_Assembly/quast/summary/
Icarus (contig browser) is saved to /home/fch/Projects/LG6/02_Assembly/quast/icarus.html
Drawing interactive Krona plots...

'NoneType' object is not iterable
Traceback (most recent call last):
File "/home/fch/miniconda3/envs/quast/bin/metaquast.py", line 427, in
return_code = main(sys.argv[1:])
File "/home/fch/miniconda3/envs/quast/bin/metaquast.py", line 417, in main
html_saver.create_meta_report(output_dirpath, json_texts)
File "/home/fch/miniconda3/envs/quast/lib/python3.7/site-packages/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/fch/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/html_saver/html_saver.py", line 363, in create_krona_charts
for section in report:
TypeError: 'NoneType' object is not iterable
ERROR! exception caught!

[RayanaFeltrin]

Hello, @ReneKat
I've also had the same exact error using metaQUAST. Did you find out how to figure it out?
Thank you in advance.

[rbtoscan]

Hello again, I went ahead and ran metaquast.py again but this time without the gene-calling -f argument. However, I got a similar exception caught:

Drawing NGA50 metaQUAST summary plot...
saved to /home/fch/Projects/LG6/02_Assembly/quast/summary/PDF/NGA50.pdf
Drawing LGA50 metaQUAST summary plot...
saved to /home/fch/Projects/LG6/02_Assembly/quast/summary/PDF/LGA50.pdf
Text versions of reports and plots for each metric (for all references and assemblies) are saved to /home/fch/Projects/LG6/02_Assembly/quast/summary/
Icarus (contig browser) is saved to /home/fch/Projects/LG6/02_Assembly/quast/icarus.html
Drawing interactive Krona plots...
'NoneType' object is not iterable
Traceback (most recent call last):
File "/home/fch/miniconda3/envs/quast/bin/metaquast.py", line 427, in
return_code = main(sys.argv[1:])
File "/home/fch/miniconda3/envs/quast/bin/metaquast.py", line 417, in main
html_saver.create_meta_report(output_dirpath, json_texts)
File "/home/fch/miniconda3/envs/quast/lib/python3.7/site-packages/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/fch/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/html_saver/html_saver.py", line 363, in create_krona_charts
for section in report:
TypeError: 'NoneType' object is not iterable
ERROR! exception caught!

facing the same issue. has this been addressed?

[RayanaFeltrin]

Hey @rbtoscan!
I had a similar problem last year as reported in #251.
The solution was to use the flag --no-krona that @alexeigurevich created as a workaround in version 5.2.0. However, since then they still didn't release a new QUAST version :/

Good luck!

[rbtoscan]

nice, thank you very much, @RayanaFeltrin!

will give it a try :)