IndexError: index 7498 is out of bounds for axis 1 with size 7498

[Sri Dewi]

Hello,
can somebody please help me?
I try to run
python conifer.py analyze --probes probes.txt --rpkm_dir /RPKM/ --output /result/analysis.hdf5 --svd 6 --write_sval /singular_values.txt

i will get this error:

[RUNNING: chr1] Calculating median RPKM
/usr/local/lib/python2.7/dist-packages/numpy-1.11.1rc1-py2.7-linux-x86_64.egg/numpy/lib/function_base.py:3578: RuntimeWarning: Invalid value encountered in median for 1 results
RuntimeWarning)
conifer.py:147: RuntimeWarning: invalid value encountered in greater_equal
probe_mask = median >= float(args.min_rpkm)
[RUNNING: chr1] Masking 7716 probes with median RPKM < 1.000000
conifer.py:157: VisibleDeprecationWarning: boolean index did not match indexed array along dimension 0; dimension is 7498 but corresponding boolean dimension is 101685
probeIDs = np.array(map(operator.itemgetter("probeID"),chr_probes))[probe_mask]
Traceback (most recent call last):
File "conifer.py", line 682, in <module>
args.func(args)
File "conifer.py", line 157, in CF_analyze
probeIDs = np.array(map(operator.itemgetter("probeID"),chr_probes))[probe_mask]
IndexError: index 7498 is out of bounds for axis 1 with size 7498

has anybody encountered this error? I have no idea where I can fix this.
Thanks in advance for the help!

Sincerely

Dewi