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Error in streaming SVD of abundance matrix #8
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Hi, Sorry for my slow response. Are you running the distributed version, or the single instance version? Do you mind sending me the output of "ls -l" for hashed_reads/ and On Thu, Nov 19, 2015 at 12:54 PM, Condomitti notifications@github.com
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Hi, Any suggestions? I have included below the content of my hashed_reads and cluster_vectors folders. ls -l hashed_reads/ ls -l cluster_vectors/ |
Hi Andres, Is it the case that you have only a single sample there? The premise of LSA On Mon, Feb 22, 2016 at 7:08 AM, Andres Baravalle notifications@github.com
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Hi Andres and Brian,
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Hi Brian, Condomitti, Brian, I'm coming to this from a computing background (not that familiar with LSA right now) as part of a multi-disciplinary team. Apparently you are right, the data we used as a test might have been from a single sample. Will do a new test tomorrow, hopefully with the right data, and will ping back. Thanks again for the help,
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Hello,
I've been trying to run LSA scripts with my own dataset but I'm getting 'float division by zero' error doesn't matter what I do with input data.
I was able to run the entire pipeline with test data but couldn't with my own set (Illumina MiSeq paired-end reads, organized in a single file in an interleaved fashion as generated by LSFScripts/merge_and_split_pair_files.py).
This is the error LSA is printing out:
Starting streaming SVD of conditioned k-mer abundance matrix
8 printing end of last log file...
9 self.add_documents(corpus)
10 File "/usr/lib/python2.7/dist-packages/gensim/models/lsimodel.py", line 387, in add_documents
11 update = Projection(self.num_terms, self.num_topics, job, extra_dims=self.extra_samples, power_iters=self.power_iters)
12 File "/usr/lib/python2.7/dist-packages/gensim/models/lsimodel.py", line 127, in init
13 extra_dims=self.extra_dims)
14 File "/usr/lib/python2.7/dist-packages/gensim/models/lsimodel.py", line 742, in stochastic_svd
15 keep = clip_spectrum(s**2, rank, discard=eps)
16 File "/usr/lib/python2.7/dist-packages/gensim/models/lsimodel.py", line 86, in clip_spectrum
17 small = 1 + len(numpy.where(rel_spectrum > min(discard, 1.0 / k))[0])
18 ZeroDivisionError: float division by zero
Is this an issue or am I doing something wrong? Apparently this error comes after Hashcounting is finished.
Thank you in advance.
Best,
Condomitti.
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