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/coordTotallength(>=_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_summaryplot 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/coordTotallength(>=_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?