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BoevaLab / SV-Bay

Detection of structural variants in cancer mate-pair and paired-end data
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Run time error #7

Closed rmurphy49 closed 6 years ago

rmurphy49 commented 7 years ago

I have the following run time error from the normal/abnormal fragments separation and clustering workflow, using the tutorial command:

File "/users/40057929/SV-Bay/src/main_clustering.py", line 89, in Process(data_file, config) File "/users/40057929/SV-Bay/src/main_clustering.py", line 80, in Process cf.PerformClustering() File "/users/40057929/SV-Bay/src/chrfragments.py", line 175, in PerformClustering utils.clust(self.fr_abn, self.chr, 'fr', self.biggest_normal, self.smallest_normal, self.config, self.flag_direction) File "/users/40057929/SV-Bay/src/utils.py", line 65, in clust clusters = cluster.Clustering(fragments, M, S, chrm, chrm, 0, config,direction) File "/users/40057929/SV-Bay/src/cluster.py", line 414, in Clustering new_clusters = KMeansSplit(cluster_for_kmeans, D) File "/users/40057929/SV-Bay/src/cluster.py", line 342, in KMeansSplit (res_my, idx_my) = kmeans2(array(zip(x)), k) File "/users/40057929/gridware/share/python/2.7.8/lib/python2.7/site-packages/scipy/cluster/vq.py", line 781, in kmeans2 return _kmeans2(data, clusters, iter, nc, _valid_miss_meth[missing]) File "/users/40057929/gridware/share/python/2.7.8/lib/python2.7/site-packages/scipy/cluster/vq.py", line 795, in _kmeans2 new_code, has_members = _vq.update_cluster_means(data, label, nc) File "scipy/cluster/_vq.pyx", line 340, in scipy.cluster._vq.update_cluster_means (scipy/cluster/_vq.c:5057) TypeError: type other than float or double not supported

Any advice?

dashainparis commented 6 years ago

Hello, if fact it seems that is some errors with version of scipy, could you please send me some sample of you data so I can check it (100-200 mb would be enough).

rmurphy49 commented 6 years ago

I have actually finished my project now and don't have access to the data anymore apologies! I hope the issue can be rectified for any further use with SV-Bay in the future however :)