Error creating files for visualization

[d-golzato]

Hi everyone,

I wanted to visually inspect the results from the fitted model of PopPUNK on a set of E.coli genomes but whenever I add the options "--cytoscape", "--microreact", "--phandango" or "--grapetree" I get the error Error creating files for visualisation: <class 'TypeError'>.

I tested this also on the Listeria monocytogenes genomes from the quickstart tutorial. I prepared the genomes by running the commands:

tar xf listeria_example.tar.bz2 paste <(ls *.contigs_velvet.fa) <(ls *.contigs_velvet.fa) > reference_list.txt

Followed by the command:

poppunk-runner.py --easy-run --r-files reference_list.txt --output lm_example --threads 4 --plot-fit 5 --min-k 13 --full-db --cytoscape

And the output is the following:

Sketching 128 genomes using 4 thread(s)
Writing sketches to file
Calculating random match chances using Monte Carlo
Calculating distances using 4 thread(s)
Fit summary:
        Number of clusters      5
        Number of datapoints    8128
        Number of assignments   32098641

Scaled component means
        [0.94726908 0.90340108]
        [0.00528333 0.07036978]
        [0.21082306 0.37437737]
        [0.12985218 0.34321457]
        [0.11504833 0.2416508 ]

Initial model-based network construction based on DBSCAN fit
Initial boundary based network construction
Decision boundary starts at (0.63,0.62)
Trying to optimise score globally
Trying to optimise score locally

Optimization terminated successfully;
The returned value satisfies the termination criteria
(using xtol =  1e-05 )
Network summary:
        Components      29
        Density 0.0899
        Transitivity    0.9994
        Score   0.9095
Writing grapetree output
Error creating files for visualisation: <class 'TypeError'>
Done

I'm using version 2.1.0 of PopPUNK and all the dependencies indicated at https://poppunk.readthedocs.io/en/latest/installation.html have been installed.

Could you help me solving this problem? Thank you!

[nickjcroucher]

Hi Davide,

This is a problem with the visualisation functions, sorry - it was fixed recently, and the commands you listed work with the version available from the GitHub repository. If you install the latest updates through git clone https://github.com/johnlees/PopPUNK and use the poppunk-runner.py script in the PopPUNK directory to run the analysis, in place of the conda-installed version, that should do the trick.

Thanks, Nick.

[d-golzato]

Hi Nick,
Thank you very much for your quick response.

I confirm it works. I was currently running PopPUNK version cloned directly from the GitHub repository. I have just pulled the most recent repository and updated graph-tools and now it runs without problems.

Many thanks,
Davide