multievolve.py: ValueError: zero-size array to reduction operation maximum which has no identity

[zlin77]

Hi,

This is my first time to use phylowgs and it is possible that I messed up with something. However, the problem is that after following README to git clone the package and compile using the following command:

g++ -o mh.o -O3 mh.cpp util.cpp gsl-config --cflags --libs

I tried to run the following command on the example inputs ssms.txt and cnvs.txt:

python2.7 multievolve.py --num-chains 4 --ssms ssm_data.txt --cnvs cnv_data.txt

Then, the following error shows up:

Traceback (most recent call last):
File "multievolve.py", line 323, in
main()
File "multievolve.py", line 319, in main
included_chains, excluded_chains = determine_chains_to_merge(chain_dirs, args['chain_inclusion_factor'])
File "multievolve.py", line 229, in determine_chains_to_merge
logSumLHs.append(scipy.misc.logsumexp(logLHs))
File "//anaconda/lib/python2.7/site-packages/numpy/lib/utils.py", line 100, in newfunc
return func(*args, **kwds)
File "//anaconda/lib/python2.7/site-packages/scipy/special/_logsumexp.py", line 101, in logsumexp
a_max = np.amax(a, axis=axis, keepdims=True)
File "//anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "//anaconda/lib/python2.7/site-packages/numpy/core/_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

Any ideas will be appreciated! Thanks so much in advance!

Best,
Ziao

[karini925]

Same exact issue, multievolve.py has previously worked on one sample and works on test data but my SSM file with 20 samples gives same error as you. Trying to figure out why... let me know if you came up with anything, thanks!

[nodanny]

I met the same error with the example data! Meanwhile, there is an error stating that "/urpath/miniconda2/envs/bioinfo/share/phylowgs/mh.o: error while loading shared libraries: libcblas.so.3: cannot open shared object file: No such file or directory".
I ran the command below and solved the error.

cd /urpath/miniconda2/envs/bioinfo/lib
ln -s libcblas.so libcblas.so.3

[karini925]

After I renamed the id column to S0 to Sn.... and made sure my SSM file was tab-delimited, the error went away and it ran as expected.

[aleighbrown]

We got this error when we forgot to compile the C++ code as an fyi.

[adhisadi]

Has anyone come up with any other solution. I have compiled the C++ code, my files are tab-delimited and id columns are named s0 to sn. I still get this error with my data (single sample) and with the example data.