NucDiff waiting for input ("ku")

[schorlton]

Issue

Thanks for the great software. When I run NucDiff, it runs successfully until the Find differences... step. Then, I get:

The difference detection between fragments step is complete
['NZ_QRIH01000033.1', 9101, 9101, 'NODE_14037_length_1602_cov_4.386555', 1280, 1280, 'insertion-multiple_copy', 1, 'struct', 1, '1.4', [['NZ_QRIH01000033.1', 9101, 9101, 'NODE_14037_length_1602_cov_4.386555', 1130, 1130, 1, [1280, 1280, 'insertion-multiple_copy', 1, '1.4']]], 'SV_133', 'SV_135']
ku

and it's waiting for input. If I hit enter, it continues and I get the same thing, then need to hit enter again. One more enter gets NucDiff to successfully exit. On all my other files, NucDiff does not require any input.

I believe this is related to this line?

NucDiff/nucdiff/generate_output.py

Line 580 in 985539a

input('ku')

I also wonder if this user was hitting the same issue: #23

Reproduction

nucdiff reference.fna test.fna reference_alignment test

Files attached:
test_data.zip

Additional info

Running NucDiff 2.0.3 from BioContainer: quay.io/biocontainers/nucdiff:2.0.3--pyh864c0ab_1

[kseniakh]

Hi Sam,

The issue that you have is related to the case when you have so rare placement of the fragments that it was not met in the real life testing examples but only in simulated data. I prefer to track such cases to be sure that they are resolved correctly.

I support the tool in my free time. And, unfortunately, now I don't have much time to look into this case. But I will return to it as soon as I can.