data conversion error

[aCoalBall]

Hi there,

I have successfully downloaded the training data using

bonito download --training

But I meet errors when converting it:

bonito convert dna_r9.4.1.hdf5 dna_r9.4.1

File "mtrand.pyx", line 4703, in numpy.random.mtrand.RandomState.permutation ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (66149, 2) + inhomogeneous part.

Is there any way to fix it?

[hoho2b]

Hi @aCoalBall, Could you please show your numpy version?

• This error is also shown in #347
• I guess your numpy version is >= 1.24.0, which raise ValueError instead of DeprecationWarning (release note).
• If that is true, this PR might fix this error: #311

[aCoalBall]

Thanks, you are right! my numpy is 1.24.2 and I have fixed the error.