neoloop-caller has some error

[yangfeizZZ]

Hi: when i run neoloop-caller follow your code,some error occur. The code is : neoloop-caller -O K562.neo-loops.txt -H K562-MboI-allReps-hg38.10K.cool --assembly K562.assemblies.txt --no-clustering --prob 0.95 The error is: /home/yangfei/.conda/envs/neoloop/lib/python3.7/site-packages/neoloop/util.py:415: RuntimeWarning: invalid value encountered in greater I don't know how to solve it.

[JSegueni]

Hi,

This seems to be just a warning message not an error message.

Are you sure you pasted the right message?

[yangfeizZZ]

Hi,

This seems to be just a warning message not an error message.

Are you sure you pasted the right message?

It is an error.when i frist run ,the error is: root INFO @ 09/09/22 17:51:54:

ARGUMENT LIST:

Output Path = M1.neo-loop.txt

Cache Folder = .cache

SV assembly = M1.assemblies.txt

Cooler List = ['M1_5000.cool']

Extended Genomic Span = 5000000bp

Balance Type = CNV

Probability threshold = 0.95

No pooling = True

Minimum marginal peaks = 2

Number of Processes = 1

Log file name = neoloop.log

--2022-09-09 17:52:01-- https://dl.dropboxusercontent.com/s/mwcdn9j4rjrb5u2/high-confidence.100million.5kb.pkl?dl=0 正在解析主机 dl.dropboxusercontent.com (dl.dropboxusercontent.com)... 199.59.150.49, 2001::a27d:2009 正在连接 dl.dropboxusercontent.com (dl.dropboxusercontent.com)|199.59.150.49|:443... 失败：连接超时。 正在连接 dl.dropboxusercontent.com (dl.dropboxusercontent.com)|2001::a27d:2009|:443... 失败：网络不可达。

when i run again.the error is: root INFO @ 09/09/22 17:54:26:

ARGUMENT LIST:

Output Path = M1.neo-loop.txt

Cache Folder = .cache

SV assembly = M1.assemblies.txt

Cooler List = ['M1_5000.cool']

Extended Genomic Span = 5000000bp

Balance Type = CNV

Probability threshold = 0.95

No pooling = True

Minimum marginal peaks = 2

Number of Processes = 1

Log file name = neoloop.log

root INFO @ 09/09/22 17:54:33: Load assembled SVs root INFO @ 09/09/22 17:54:33: Current resolution: 5000 root INFO @ 09/09/22 17:54:33: Calculate the global average contact frequencies at each genomic distance ... /home/marh/miniconda3/envs/neoloop/lib/python3.7/site-packages/neoloop/util.py:415: RuntimeWarning: invalid value encountered in greater tmp = np.isfinite(weights) & (weights > 0) root INFO @ 09/09/22 17:57:05: Done [Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.