Metaquast 5.2 summary error

[JianxinS0806]

When I run quast successfully, the following error occurs in the summarizing result stage

Summarizing results...
Drawing # contigs metaQUAST summary plot...
saved to /media/jxs/Data/metagenomic_data/BN221214NY01S03N1/rawdata/1883-1/megahit_out/metaquast_out/summary/PDF/num_contigs.pdf
Drawing Largest contig metaQUAST summary plot...
saved to /media/jxs/Data/metagenomic_data/BN221214NY01S03N1/rawdata/1883-1/megahit_out/metaquast_out/summary/PDF/Largest_contig.pdf
Drawing Total length metaQUAST summary plot...
saved to /media/jxs/Data/metagenomic_data/BN221214NY01S03N1/rawdata/1883-1/megahit_out/metaquast_out/summary/PDF/Total_length.pdf
Drawing Largest alignment metaQUAST summary plot...
saved to /media/jxs/Data/metagenomic_data/BN221214NY01S03N1/rawdata/1883-1/megahit_out/metaquast_out/summary/PDF/Largest_alignment.pdf
Drawing Total aligned length metaQUAST summary plot...
saved to /media/jxs/Data/metagenomic_data/BN221214NY01S03N1/rawdata/1883-1/megahit_out/metaquast_out/summary/PDF/Total_aligned_length.pdf
Drawing Total length (>= 1000 bp) metaQUAST summary plot...

[Errno 22] Invalid parameter: '/media/jxs/Data/metagenomic_data/BN221214NY01S03N1/rawdata/1883-1/megahit_out/metaquast_out/summary/coordTotal_length_(>=1000_bp).json'
Traceback (most recent call last):
File "/home/jxs/anaconda3/envs/quast/bin/metaquast", line 427, in
return_code = main(sys.argv[1:])
File "/home/jxs/anaconda3/envs/quast/bin/metaquast", line 411, in main
output_dirpath_per_ref, metrics_for_plots, misassembly_metrics, full_ref_names)
File "/home/jxs/anaconda3/envs/quast/opt/quast-5.2.0/quast_libs/create_meta_summary.py", line 108, in do
print_all_refs=True, logger=logger)
File "/home/jxs/anaconda3/envs/quast/opt/quast-5.2.0/quast_libs/plotter.py", line 685, in draw_meta_summary_plot
title.replace(' ', ''), labels, refs_for_html)
File "/home/jxs/anaconda3/envs/quast/opt/quast-5.2.0/quast_libs/html_saver/html_saver.py", line 451, in save_meta_summary
json_fpath = json_saver.save_meta_summary(results_dirpath, coord_x, coord_y, name_coord, labels, refs)
File "/home/jxs/anaconda3/envs/quast/opt/quast-5.2.0/quast_libs/html_saver/json_saver.py", line 169, in save_meta_summary
'refnames': refs_names
File "/home/jxs/anaconda3/envs/quast/opt/quast-5.2.0/quast_libs/html_saver/json_saver.py", line 50, in save
json_file = open(fpath, 'w')
OSError: [Errno 22] Invalid parameter
: '/media/jxs/Data/metagenomic_data/BN221214NY01S03N1/rawdata/1883-1/megahit_out/metaquast_out/summary/coordTotal_length_(>=_1000_bp).json'
metaquast.log
This confuses me a lot. And hope to get your help, thanks.

[asl]

Hello

It seems your output directory is on some removable storage and the file system there does not allow special symbols in paths (e.g. ">" or "=" like here). I would suggest you to move output directory elsewhere.

[JianxinS0806]

Thank you very much for your answer! According to the method you suggested, I have successfully solved the previous problem. Meanwhile another new problem popped up, and I noticed that ReneKat had the same problem(ERROR!exception caught! in QUAST v5.2.0 #216). The specific error is as follows:

Drawing LGA50 metaQUAST summary plot...
saved to /home/jxs/metaquast_out/summary/PDF/LGA50.pdf

Text versions of reports and plots for each metric (for all references and assemblies) are saved to /home/jxs/metaquast_out/summary/
Icarus (contig browser) is saved to /home/jxs/metaquast_out/icarus.html
Drawing interactive Krona plots...

'NoneType' object is not iterable
Traceback (most recent call last):
File "/home/jxs/anaconda3/envs/quast/bin/metaquast", line 427, in
return_code = main(sys.argv[1:])
File "/home/jxs/anaconda3/envs/quast/bin/metaquast", line 417, in main
html_saver.create_meta_report(output_dirpath, json_texts)
File "/home/jxs/anaconda3/envs/quast/opt/quast-5.2.0/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/jxs/anaconda3/envs/quast/opt/quast-5.2.0/quast_libs/html_saver/html_saver.py", line 363, in create_krona_charts
for section in report:
TypeError: 'NoneType' object is not iterable
metaquast_2.log
I would be very grateful for any help that you provide.

[RayanaFeltrin]

Hello, @JianxinS0806
I've also had the same exact error using metaQUAST. Did you find out how to figure it out?
Thank you in advance.

[Rose0498]

Hi,
I was able to complete the Metaquast analysis, however the HTML report isn't loading

can anyone help me with the same?