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brianhie / scanorama

Panoramic stitching of single cell data
http://scanorama.csail.mit.edu
MIT License
265 stars 49 forks source link

Restarting kernel... #120

Closed auesro closed 2 years ago

auesro commented 2 years ago

I am trying to correct_scanpy a dataset made of 4 batches with 32269 cells and 23546 genes in total. I am running into a "Restarting kernel..." error in Spyder that stops everything:

Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53) 
Type "copyright", "credits" or "license" for more information.

IPython 7.32.0 -- An enhanced Interactive Python.

runcell(0, '/home/auesro/Desktop/Cell_Ranger/Merge/AER_Merge_v2.py')

runcell('SCANORAMA CORRECTION IN ALL GENES', '/home/auesro/Desktop/Cell_Ranger/Merge/AER_Merge_v2.py')
Found 23546 genes among all datasets
[[0.         0.830794   0.82057985 0.65576613]
 [0.         0.         0.8549192  0.69690722]
 [0.         0.         0.         0.79336977]
 [0.         0.         0.         0.        ]]
Processing datasets (1, 2)
Processing datasets (0, 1)
Processing datasets (0, 2)

Restarting kernel...

The workstation has 64GB RAM and 16 CPUs.

Any ideas?