THOR- Issue in regenerating report

[chaochungkuo]

Below is the error message I got when I set --report in the command.

I will also check it later.

Call DPs on whole genome.
Computing read extension sizes for ChIP-seq profiles
Compute GC-content
Compute factors
Normalize input of Signal 0, Rep 0 with factor 0.767
Normalize input of Signal 0, Rep 1 with factor 0.767
Normalize input of Signal 1, Rep 0 with factor 0.769
Normalize input of Signal 1, Rep 1 with factor 0.769
Use global TMM approach 
Traceback (most recent call last):
  File "/work/ck687463/bin/rgt-THOR", line 11, in <module>
    load_entry_point('RGT==0.10.0', 'console_scripts', 'rgt-THOR')()
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/RGT-0.10.0-py2.7.egg/rgt/THOR/THOR.py", line 157, in main
    chrom_sizes, dims, inputs, tracker)
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/RGT-0.10.0-py2.7.egg/rgt/THOR/THOR.py", line 81, in train_HMM
    report=options.report, poisson=options.poisson)
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/RGT-0.10.0-py2.7.egg/rgt/THOR/dpc_help.py", line 197, in _fit_mean_var_distr
    _plot_func(plot_data, outputdir)
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/RGT-0.10.0-py2.7.egg/rgt/THOR/dpc_help.py", line 108, in _plot_func
    maxs.append(max(tmp[tmp < np.percentile(tmp, 90)]))
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/numpy/lib/function_base.py", line 4116, in percentile
    interpolation=interpolation)
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3858, in _ureduce
    r = func(a, **kwargs)
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/numpy/lib/function_base.py", line 4233, in _percentile
    x1 = take(ap, indices_below, axis=axis) * weights_below
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 134, in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
  File "/rwthfs/rz/cluster/work/ck687463/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
    return getattr(obj, method)(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.

[fabio-t]

@jovesus were you able to re-run the experiment that caused this?

[npavlovikj]

Hi,

I just downloaded "RGT-0.11.4", and I am encountering the same error when running "rgt-THOR" with "--report". Is there some workaround for this?

Thank you, Natasha

[laijen000]

Hi all! I am getting the same IndexError with version 0.13.1 and I ran with the command --report. Has this issue been resolved? Or am I unable to run with --report? Thank you!