Issue visualizing squiggles with recent fast5 file

[mriekje]

Hi,

I'm trying to visualize some squiggles from a recent fast5 file using SquigglePlot and the following command: python3 SquigglePlot.py -m -i /Users/marieke/data/test/FAO01221_pass_d7290dd7_3.fast5

However, when I try this it gives me the following error:

Traceback (most recent call last):
  File "/Users/marieke/SquiggleKit/SquigglePlot.py", line 365, in <module>
    main()
  File "/Users/marieke/SquiggleKit/SquigglePlot.py", line 229, in main
    sig = sigs[args.readID]
KeyError: None

Trying to run SquigglePull on the same file gives me the same h5py error as #41.

The file was created with MinKNOW 20.10.6. I've tried using Python 2 and 3.

Any idea what's going on here and is there a fix for it? Thanks, Marieke.

[Psy-Fer]

Hey, welcome to github.

So the error in squigglePlot seems to a missing argument, for the specific readID you want to plot in the fast5 file.

Try copying the fast5 file into its own folder, then running the command with -m and -p /path/to/folder/

See if it works then?

The rest I'll be investigating soon. Thanks for the issue

Cheers, James

[hanost]

H, I am having this issue as well, but a different error message.

Traceback (most recent call last):
  File "/home/work/hwackel/Nanopore_project/SquiggleKit/SquigglePlot.py", line 433, in <module>
    main()
  File "/home/work/hwackel/Nanopore_project/SquiggleKit/SquigglePlot.py", line 275, in main
    view_sig(args, sig, read, fast5)
  File "/home/work/hwackel/Nanopore_project/SquiggleKit/SquigglePlot.py", line 421, in view_sig
    filename = os.path.join(args.save_path, "{}_dpi_{}_{}".format(name, args.dpi, args.save))
  File "/home/work/hwackel/.conda/envs/nanopore/lib/python3.9/posixpath.py", line 76, in join
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType

[Psy-Fer]

Hello,

Could you please give me the command you are using?

At a quick glance this looks like --save was used without a valid file or --save_path path.

Cheers, James