Error

[MenggeZhao]

[MM/DD/YYYY HH:MM:SS (XX.XXX MB)] N95_fragment_length is: -1
Traceback (most recent call last):
File "linkedsv.py", line 278, in
main()
File "linkedsv.py", line 43, in main
detect_increased_fragment_ends(args, dbo_args, endpoint_args)
File "linkedsv.py", line 178, in detect_increased_fragment_ends
cluster_reads.cluster_reads(args, dbo_args, endpoint_args)
File "/LinkedSV/scripts/cluster_reads.py", line 62, in cluster_reads
global_distribution.estimate_global_distribution (args, dbo_args, endpoint_a rgs, endpoint_args.tmpbcd22_file, is_fast_mode = True)
File "/LinkedSV/scripts/global_distribution.py", line 116, in estimate_global_distribution
get_fragment_parameters(args, dbo_args, endpoint_args, global_dist_fp, targe t_bcd22_file, is_fast_mode)
File "LinkedSV/scripts/global_distribution.py", line 196, in get_fragment_parameters
args.fragment_length_lmda = fit_geometric_distribution(frm_length_list, read pair = False)
File "LinkedSV/scripts/global_distribution.py", line 154, in fit_geometric_distribution
k = np.percentile(length_list, cdf2)
File "bin/anaconda/envs/py2/lib/python2.7/site-pac kages/numpy/lib/function_base.py", line 3707, in percentile
a, q, axis, out, overwrite_input, interpolation, keepdims)
File "anaconda/envs/py2/lib/python2.7/site-pac kages/numpy/lib/function_base.py", line 3826, in _quantile_unchecked
interpolation=interpolation)
File "anaconda/envs/py2/lib/python2.7/site-pac kages/numpy/lib/function_base.py", line 3405, in _ureduce
r = func(a, **kwargs)
File "anaconda/envs/py2/lib/python2.7/site-pac kages/numpy/lib/function_base.py", line 3941, in _quantile_ureduce_func
x1 = take(ap, indices_below, axis=axis) * weights_below
File "anaconda/envs/py2/lib/python2.7/site-pac kages/numpy/core/fromnumeric.py", line 189, in take
return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
File "anaconda/envs/py2/lib/python2.7/site-pac kages/numpy/core/fromnumeric.py", line 56, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.

[fangli80]

Fixed. Please pull the latest version.

Thank you.

[Martaprf]

Hi,

I am getting the same error and I don't know why. Can someone help me.
[06/09/2021 16:02:18 (143.557 MB)] N95_fragment_length is: -1
Traceback (most recent call last):
File "/home/mferreira/programs/LinkedSV/linkedsv.py", line 313, in
main()
File "/home/mferreira/programs/LinkedSV/linkedsv.py", line 47, in main
detect_increased_fragment_ends(args, dbo_args, endpoint_args)
File "/home/mferreira/programs/LinkedSV/linkedsv.py", line 208, in detect_increased_fragment_ends
global_distribution.estimate_global_distribution(args, dbo_args, endpoint_args, endpoint_args.bcd22_file)
File "/home/mferreira/programs/LinkedSV/scripts/global_distribution.py", line 133, in estimate_global_distribution
get_fragment_parameters(args, dbo_args, endpoint_args, global_dist_fp, target_bcd22_file, is_fast_mode)
File "/home/mferreira/programs/LinkedSV/scripts/global_distribution.py", line 213, in get_fragment_parameters
args.fragment_length_lmda = fit_geometric_distribution(frm_length_list, readpair = False)
File "/home/mferreira/programs/LinkedSV/scripts/global_distribution.py", line 171, in fit_geometric_distribution
k = np.percentile(length_list, cdf2)
File "<array_function internals>", line 6, in percentile
File "/usr/local/lib/python3.6/dist-packages/numpy/lib/function_base.py", line 3706, in percentile
a, q, axis, out, overwrite_input, interpolation, keepdims)
File "/usr/local/lib/python3.6/dist-packages/numpy/lib/function_base.py", line 3826, in _quantile_unchecked
interpolation=interpolation)
File "/usr/local/lib/python3.6/dist-packages/numpy/lib/function_base.py", line 3403, in _ureduce
r = func(a, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/numpy/lib/function_base.py", line 3941, in _quantile_ureduce_func
x1 = take(ap, indices_below, axis=axis) * weights_below
File "<array_function internals>", line 6, in take
File "/usr/local/lib/python3.6/dist-packages/numpy/core/fromnumeric.py", line 194, in take
return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
File "/usr/local/lib/python3.6/dist-packages/numpy/core/fromnumeric.py", line 61, in _wrapfunc
return bound(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.

Thanks

[fangli80]

Hi, is your data whole-genome sequencing or targeted sequencing?

[Martaprf]

It is whole exome sequencing