RuntimeWarning in Circle-Map Realign

[hanssli]

@iprada ,
Hello!
I was performing the Circle-Map Realign tutorial, and encountered a few warnings.

[bam_sort_core] merging from 4 files and 6 in-memory blocks...
2024-03-31 18:50:47: Realigning reads using Circle-Map

2024-03-31 18:50:47: Clustering structural variant reads

2024-03-31 18:52:19: Splitting clusters to to processors

600it [1:33:27, 9.35s/it] ████████████████| 600/600 [1:33:27<00:00, 252.17s/it]
100%|███████████████████████████████████████| 600/600 [1:33:27<00:00, 9.35s/it]
2024-03-31 20:25:48: Writting final output to disk
2024-03-31 20:25:49: Finished!
2024-03-31 20:25:49: Circle-Map Realign finished indentifying circles in 95.02959271669388

2024-03-31 20:25:49: Circle-Map has identified 17168 circles

Computing the coverage of the identified eccDNA
Merging intervals for coverage computation
Computing coverage on interval 1:696529-247911309
/home/h/miniconda3/envs/circlemap/lib/python3.7/site-packages/circlemap/Coverage.py:151: RuntimeWarning: invalid value encountered in ulong_scalars
end_coverage_ratio = np.sum(region_array[-self.ilen:]) / np.sum(ext_array[-(self.ilen + self.ext):])
/home/h/miniconda3/envs/circlemap/lib/python3.7/site-packages/circlemap/Coverage.py:150: RuntimeWarning: invalid value encountered in ulong_scalars
ext_array[0:(self.ilen + self.ext)])

and the following waring:

**/home/h/miniconda3/envs/circlemap/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3257: RuntimeWarning: Mean of empty slice.
out=out, kwargs)
/home/h/miniconda3/envs/circlemap/lib/python3.7/site-packages/numpy/core/_methods.py:161: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/h/miniconda3/envs/circlemap/lib/python3.7/site-packages/numpy/core/_methods.py:217: RuntimeWarning: Degrees of freedom <= 0 for slice
keepdims=keepdims)
/home/h/miniconda3/envs/circlemap/lib/python3.7/site-packages/numpy/core/_methods.py:186: RuntimeWarning: invalid value encountered in true_divide
arrmean, rcount, out=arrmean, casting='unsafe', subok=False)
/home/h/miniconda3/envs/circlemap/lib/python3.7/site-packages/numpy/core/_methods.py:209: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)

All of "Computing coverage on interval ***" looks completed.

Is it safe to ignore these warnings?

Thanks and best wishes,
Han

[iprada]

Hi Han,

It should be safe to ignore them. This is when calculating the coverage metrics and does not affect circle calls.

best,

Iñigo

[hanssli]

@iprada ,
That's fine.
For the identified circles, what's the next step to handle with them? How to count the copies for same circle? How to compare two groups?
I would appreciate it if you could give any suggestions?

Thanks and best wishes,
Han

[iprada]

Hi Han,

The questions you are asking are unresolved scientific challenges, I am afraid. I cannot help without knowing more. But sounds like you might need to collaborate with an expert to address them.

best,

Iñigo