Failed quality curve generation

[satkinson0115]

Hi,

I'm running into an error trying to produce the quality plots with iu-filter-quality-minoche. This is the command I ran and the error I received:

#!/bin/bash
source activate anvio-7
iu-gen-configs samples_ada.txt -o 01_QC_minoche/
for ini in 01_QC_minoche/*.ini;
do iu-filter-quality-minoche $ini --visualize-quality-curves;
done

Quality scores visualization in progress: FAILED_REASON_N                    Traceback (most recent call last):
  File "/home/saatkinson/anaconda3/envs/anvio-7/bin/iu-filter-quality-minoche", line 314, in <module>
    sys.exit(main(config, args))
  File "/home/saatkinson/anaconda3/envs/anvio-7/bin/iu-filter-quality-minoche", line 265, in main
    title = 'Mean PHRED scores for pairs tagged as "%s"' % entry_type)
  File "/home/saatkinson/anaconda3/envs/anvio-7/lib/python3.6/site-packages/IlluminaUtils/utils/helperfunctions.py", l
ine 558, in visualize_qual_stats_dict
    subplots[tile] = plt.subplot(next(gs))
TypeError: 'Gs' object is not an iterator

All the other files associated with Minoche seem to have been generated, just not the plots.

Any help getting the quality plots to generate would be most appreciated! Thanks, Samantha

[meren]

Hi @satkinson0115,

Thanks for the report. I fixed the error (at least I think I did). Now I will make a new release and then will ask you to update illumina-utils installation.

[meren]

OK, @satkinson0115, please run this command in your anvi'o environment:

pip install --upgrade illumina-utils==2.11

If you are using Mac and end up geting errors while compiling Levenshtein, first run these, and run the same command above again:

export CC=/usr/bin/clang
export CXX=/usr/bin/clang++

Best,