Open samarth51 opened 8 years ago
Hello, Samarth!
it seems that you do not have bam file for chr13. In folder working_dir/sam_files_dir/ should be bam files split by chromosome. If you do not want to perform analysis in chromosome 13, you should delete it from the list of the chromosomes in field 'chromosomes :' in config file.
Hope it would help!
2016-04-07 16:23 GMT+03:00 Samarth Kulshrestha notifications@github.com:
Hi, I am trying to run example data using conf.yaml provided within SV-Bay package. I have changed all essential paths but facing an error during program execution. Can you please look into this problem.
Command: python -B src/main_clustering.py -c config/config.yaml
Traceback (most recent call last): File "../SV-Bay-master/src/main_clustering.py", line 96, in stats_temp_file = open(stats_temp_fname, 'r') IOError: [Errno 2] No such file or directory: '/tmp/stats_chr13.tmp'
Thanks Samarth Kulshrestha
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Best regards,
Iakovishina Daria
Thanks for your quick response. Yes, you point it right that i do not have bam for chr13 and i made it correct by editing my config.yaml file. But again i face trouble when i execute the edited version of my config file. Error says:
File "scipy/cluster/_vq.pyx", line 340, in scipy.cluster._vq.update_cluster_means (scipy/cluster/_vq.c:4654) TypeError: type other than float or double not supported
Can you please look into this new error..
Thanks again. Samarth Kulshrestha
Hi Samarth,
I think it's something wrong with version of python or scipy, can you show me which version do you use.
Did you try to run SV-Bay on test data?
2016-04-08 9:14 GMT+03:00 Samarth Kulshrestha notifications@github.com:
Thanks for your quick response. Yes, you point it right that i do not have bam for chr13 and i made it correct by editing my config.yaml file. But again i face trouble when i execute the edited version of my config file. Error says:
File "scipy/cluster/_vq.pyx", line 340, in scipy.cluster._vq.update_cluster_means (scipy/cluster/_vq.c:4654) TypeError: type other than float or double not supported
Can you please look into this new error..
Thanks again. Samarth Kulshrestha
— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/InstitutCurie/SV-Bay/issues/2#issuecomment-207234395
Best regards,
Iakovishina Daria
Actually i am trying to set up a run on SV-Bay test data itself. Version information: Python version 2.7.7 Scipy version 0.17.0
Hi,
I too am running into similar error while running command in the test data-set. Seems like the kmeans from scipy.cluster.vq.kmeans implementation is causing the trouble as seen in here http://stackoverflow.com/questions/34084142/python-3-most-common-color-in-image-kmeans-data-type-match but really don't know how to implement in the cluster.py script.
Regards, Saile
Hello,
I am running into the same error message. Did any of you guys solve it?
Thanks, Jungmin
Traceback (most recent call last):
File "/home/jc2545/programs/SV-Bay/src/main_clustering.py", line 89, in <module>
Process(data_file, config)
File "/home/jc2545/programs/SV-Bay/src/main_clustering.py", line 80, in Process
cf.PerformClustering()
File "/ycga-ba/home/jc2545/programs/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 "/ycga-ba/home/jc2545/programs/SV-Bay/src/utils.py", line 65, in clust
clusters = cluster.Clustering(fragments, M, S, chrm, chrm, 0, config,direction)
File "/ycga-ba/home/jc2545/programs/SV-Bay/src/cluster.py", line 414, in Clustering
new_clusters = KMeansSplit(cluster_for_kmeans, D)
File "/ycga-ba/home/jc2545/programs/SV-Bay/src/cluster.py", line 342, in KMeansSplit
(res_my, idx_my) = kmeans2(array(zip(x)), k)
File "/home/jc2545/.local/lib/python2.7/site-packages/scipy/cluster/vq.py", line 772, in kmeans2
return _kmeans2(data, clusters, iter, nc, _valid_miss_meth[missing])
File "/home/jc2545/.local/lib/python2.7/site-packages/scipy/cluster/vq.py", line 786, in _kmeans2
new_code, has_members = _vq.update_cluster_means(data, label, nc)
File "scipy/cluster/_vq.pyx", line 347, in scipy.cluster._vq.update_cluster_means (scipy/cluster/_vq.c:4550)
TypeError: type other than float or double not supported
Hi,samarth51 and jungminchoi: I indeed get some errors while running SV-Bay first step (main_clustering.py)on my own data, can you give me your all test data? I wonder know why own data have some problem. thanks
I got the same error like jungminchoi ,can some one fix this?
I too have been facing similar problem when trying to train the data using bag of words model. and I have got the following errors.
File "findFeatures.py", line 54, in
Hi, I am trying to run example data using conf.yaml provided within SV-Bay package. I have changed all essential paths but facing an error during program execution. Can you please look into this problem.
Command: python -B src/main_clustering.py -c config/config.yaml
Traceback (most recent call last): File "../SV-Bay-master/src/main_clustering.py", line 96, in
stats_temp_file = open(stats_temp_fname, 'r')
IOError: [Errno 2] No such file or directory: '/tmp/stats_chr13.tmp'
Thanks Samarth Kulshrestha