TypeError: get_input() got an unexpected keyword argument 'keep_supp'

[os103]

Hi,

I get the following error message when running nano plot. I installed via conda and have tried 'conda upgrade NanoPlot'.

Thanks!
Orie

If you read this then NanoPlot 1.39.0 has crashed :-(
Please try updating NanoPlot and see if that helps...

If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues
If you could include the log file that would be really helpful.
Thanks!

Traceback (most recent call last):
File "/home/o/os103/miniconda3/envs/nanoplot-venv/bin/NanoPlot", line 10, in
sys.exit(main())
File "/home/o/os103/miniconda3/envs/nanoplot-venv/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 67, in main
keep_supp=not (args.no_supplementary))
TypeError: get_input() got an unexpected keyword argument 'keep_supp'

[Wouter De Coster]

Can you try upgrading the nanoget module using conda?

[os103]

I did see an earlier post where someone had a similar problem resolved via upgrading nano get. I tried that last night and it didn’t work. I’ve just tried it again but from within the nano plot virtual environment I’ve created (I don’t know if this will make a difference, I’m a novice with command line). I got the following output after the update but still NanoPlot is giving the same error. ***@***.*** ~]$ conda activate nanoplot-venv (nanoplot-venv) ***@***.*** ~]$ conda upgrade nanoget Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/o/os103/miniconda3/envs/nanoplot-venv added / updated specs: - nanoget The following packages will be downloaded: package | build ---------------------------|----------------- nss-3.77 | h2350873_0 2.1 MB conda-forge ------------------------------------------------------------ Total: 2.1 MB The following packages will be UPDATED: nss 3.76-h2350873_0 --> 3.77-h2350873_0 Proceed ([y]/n)? y Downloading and Extracting Packages nss-3.77 | 2.1 MB | ##################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (nanoplot-venv) ***@***.*** fastq_reads]$ NanoPlot --fastq 12-sample-no-bead-1-cat.fastq If you read this then NanoPlot 1.39.0 has crashed :-( Please try updating NanoPlot and see if that helps... If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues If you could include the log file that would be really helpful. Thanks! Traceback (most recent call last): File "/home/o/os103/miniconda3/envs/nanoplot-venv/bin/NanoPlot", line 10, in <module> sys.exit(main()) File "/home/o/os103/miniconda3/envs/nanoplot-venv/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 67, in main keep_supp=not (args.no_supplementary)) TypeError: get_input() got an unexpected keyword argument 'keep_supp' (nanoplot-venv) ***@***.*** fastq_reads]$ On 31 Mar 2022, at 21:36, Wouter De Coster ***@***.******@***.***>> wrote: Can you try upgrading the nanoget module using conda? — Reply to this email directly, view it on GitHub<#291 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO6FJMLPBOAXN3DATNS7SADVCYEEJANCNFSM5SGAWGAA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Wouter De Coster]

Hmm, remarkable. Could it be that there is an older nanoget module that somehow gets precedence?
You could try python -c "import nanoget ; print(nanoget.__version__)" and see if that matches with what you recently installed.

Maybe pip uninstall nanoget will remove an older installation.