jlevy44
commented
7 years ago Seems like factor Analysis ("factor" option) should not be run on this genome (genome too large or too many scaffolds). Try just running kpca. I may be able to fix this using other dimensionality reduction techniques from outside scikit learn, but those should be implemented post-v1
[7e/4f92f5] Submitted process > genClusterMatrix_kmerPrevalence (1) FAN_r11_split.kcount.fa [93/956254] Submitted process > transform_main (2) [df/56161c] Submitted process > transform_main (1) ERROR ~ Error executing process > 'transform_main (1)'
Caused by: Process
transform_main (1)terminated with an error exit status (1)Command executed:
!/bin/bash
cd /global/projectb/scratch/sgordon/polysCRACKER/run_dirs/OctoStrawberry.250kb.k23 python subgenomeClusteringInterface.py transform_main 1 ./recluster_files/ factor 2 cosine
Command exit status: 1
Command output: (empty)
Command exit status: 1
Command output: (empty)
Command error: Traceback (most recent call last): File "subgenomeClusteringInterface.py", line 1599, in
main()
File "subgenomeClusteringInterface.py", line 1597, in main
optionsfunct
File "subgenomeClusteringInterface.py", line 365, in transform_main
transform_plot((main,reclusterFolder,model,n_subgenomes,metric))
File "subgenomeClusteringInterface.py", line 445, in transform_plot
data = KernelPCA(n_components=499).fit_transform(data)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/sklearn/decomposition/kernel_pca.py", line 260, in fit_transform
self.fit(X, params)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/sklearn/decomposition/kernel_pca.py", line 236, in fit
K = self._get_kernel(X)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/sklearn/decomposition/kernel_pca.py", line 164, in _get_kernel
params)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/sklearn/metrics/pairwise.py", line 1399, in pairwise_kernels
return _parallel_pairwise(X, Y, func, n_jobs, kwds)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/sklearn/metrics/pairwise.py", line 1083, in _parallel_pairwise
return func(X, Y, kwds)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/sklearn/metrics/pairwise.py", line 735, in linear_kernel
return safe_sparse_dot(X, Y.T, dense_output=True)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/sklearn/utils/extmath.py", line 186, in safe_sparse_dot
ret = ret.toarray()
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/scipy/sparse/compressed.py", line 964, in toarray
return self.tocoo(copy=False).toarray(order=order, out=out)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/scipy/sparse/coo.py", line 252, in toarray
B = self._process_toarray_args(order, out)
File "/global/homes/s/sgordon/.conda/envs/polysCRACKER090617/lib/python2.7/site-packages/scipy/sparse/base.py", line 1039, in _process_toarray_args
return np.zeros(self.shape, dtype=self.dtype, order=order)
MemoryError
.command.run.1: line 99: 23466 Terminated nxf_trace "$pid" .command.trace
Work dir: /global/projectb/scratch/sgordon/polysCRACKER/run_dirs/OctoStrawberry.250kb.k23/work/df/56161cf1e10d9bb0f217bf78cc03e7
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out-- Check '.nextflow.log' file for details WARN: Killing pending tasks (1)