Comments (11)
carloelle
commented on August 14, 2024
2
Hi,
I had the same issue but I work it around using older versions of numpy and h5py. I'm using python v3.7.
@marzamKI try to uninstall numpy and h5py and then do:
pip install h5py==2.10.0
pip install numpy==1.19.5
In my case, when I run solo jsonfile.json dataset.loom again, I don't have the TypeError: Indexing arrays must have integer anymore, solo finish preprocessing of the data and start training of the neural network.
It seems to be an issue of h5py/numpy, see here.
Best,
Carlo
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njbernstein
commented on August 14, 2024
I haven't seen the error before. I think your indexes must be cast to integers. I can try to help troubleshoot if you are willing to send me your data or a subset of it.
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marzamKI
commented on August 14, 2024
Hey,
Thank you for your prompt reply!
I'm using the loom files from Linnarsson lab (http://loom.linnarssonlab.org/) - in particular the L6_Immature_Neurons, tho I suspect I'd get the same error with the others as well..
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scSeqLiubice
commented on August 14, 2024
Hi @marzamKI, @njbernstein,
i am running into the exact same problems when using solo on prefiltered loomfiles from the kallisto|bustools python implementation. @marzamKI, did you find a solution to your problem?
This is the Loomfile structure, if it helps by any chance:
>>> Bl6.adata
AnnData object with n_obs × n_vars = 198891 × 55487
var: 'gene_name'
layers: 'matrix', 'spliced', 'unspliced'
>>> adata.var.index
Index(['ENSMUSG00000079800.2', 'ENSMUSG00000079192.2', 'ENSMUSG00000094799.1',
'ENSMUSG00000079794.2', 'ENSMUSG00000095092.1', 'ENSMUSG00000079190.3',
'ENSMUSG00000095672.1', 'ENSMUSG00000094514.1', 'ENSMUSG00000095787.1',
'ENSMUSG00000095250.1',
...
'ENSMUSG00000103524.1', 'ENSMUSG00000103796.1', 'ENSMUSG00000103757.1',
'ENSMUSG00000106618.1', 'ENSMUSG00000118466.1', 'ENSMUSG00000118447.1',
'ENSMUSG00000118422.1', 'ENSMUSG00000118472.1', 'ENSMUSG00000118404.1',
'ENSMUSG00000118417.1'],
dtype='object', length=55487)
>>> adata.obs.index
Index(['AAACCCAAGAAACCCG', 'AAACCCAAGACAACTA', 'AAACCCAAGACGCAGT',
'AAACCCAAGACGGTTG', 'AAACCCAAGACTCTTG', 'AAACCCAAGAGCAACC',
'AAACCCAAGAGTCTGG', 'AAACCCAAGAGTCTTC', 'AAACCCAAGCACCGTC',
'AAACCCAAGCACTCGC',
...
'TTTGTTGTCTCAACGA', 'TTTGTTGTCTCATTTG', 'TTTGTTGTCTGGCTGG',
'TTTGTTGTCTGTAACG', 'TTTGTTGTCTGTCTCG', 'TTTGTTGTCTGTGCAA',
'TTTGTTGTCTGTGCTC', 'TTTGTTGTCTGTTGGA', 'TTTGTTGTCTTACTGT',
'TTTGTTGTCTTCACGC'],
dtype='object', length=198891)
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njbernstein
commented on August 14, 2024
So sorry about the slow response. Working on this today.
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njbernstein
commented on August 14, 2024
@marzamKI @scSeqLiubice I'm unable to recreate this error with the L6_Immature_Neurons loom file from http://loom.linnarssonlab.org/.
Do you get the same results if you run the following:
import scvi
from scvi.dataset import AnnDatasetFromAnnData, LoomDataset, \
GeneExpressionDataset, Dataset10X
scvi_data = LoomDataset(data_path)
on its own?
Again sorry about the slow response.
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njbernstein
commented on August 14, 2024
Which version of solo-sc are you both using? If not using the current version in master could you try using that version?
Here is how to install it:
git clone [email protected]:calico/solo.git && cd solo && conda create -n solo python=3.6 && conda activate solo && pip install -e .
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scSeqLiubice
commented on August 14, 2024
Hi @njbernstein,
really appreciate your response!
I'm using solo-sc : 0.6, but i did not use conda for installing and instead directly used pip install -e .
I tried using scvi, and i am getting the same error while removing non expressing cells. So maybe this issue is more scvi related?
>>> scvi_data=LoomDataset(pth + '/counts_unfiltered.Bl6.46/adata.loom')
[2021-02-04 10:08:47,833] INFO - scvi.dataset.loom | Preprocessing dataset
[2021-02-04 10:11:47,726] WARNING - scvi.dataset.loom | Removing non-expressing cells
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.8/site-packages/scvi/dataset/loom.py", line 62, in __init__
super().__init__(
File "/usr/local/lib/python3.8/site-packages/scvi/dataset/dataset.py", line 2026, in __init__
self.populate()
File "/usr/local/lib/python3.8/site-packages/scvi/dataset/loom.py", line 138, in populate
data = ds[:, select].T # change matrix to cells by genes
File "/usr/local/lib/python3.8/site-packages/loompy/loompy.py", line 206, in __getitem__
return self.layers[""][slice_]
File "/usr/local/lib/python3.8/site-packages/loompy/loom_layer.py", line 88, in __getitem__
return self.ds._file['/matrix'].__getitem__(slice)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/usr/local/lib/python3.8/site-packages/h5py/_hl/dataset.py", line 777, in __getitem__
selection = sel.select(self.shape, args, dataset=self)
File "/usr/local/lib/python3.8/site-packages/h5py/_hl/selections.py", line 82, in select
return selector.make_selection(args)
File "h5py/_selector.pyx", line 272, in h5py._selector.Selector.make_selection
File "h5py/_selector.pyx", line 183, in h5py._selector.Selector.apply_args
TypeError: Indexing arrays must have integer dtypes
Package incompatibilities? I'm using scvi : 0.6.7
Thanks for your work on this!
Edit:
I reread your comment and saw that you specifically create a Python3.6 env. I installed it into python3.8, i will use the approach for python3.6 and retry it again.
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njbernstein
commented on August 14, 2024
@scSeqLiubice 0.6.7 should work. I'm gonna change the default to that.
Can you preprocess your dataset to remove empty cells?
If not can you can send me your data so I can troubleshoot more easily?
@marzamKI I believe changing the scVI version to 0.6.7 should solve your issue.
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ymahmoud
commented on August 14, 2024
Hi,
I had the same issue but I work it around using older versions of numpy and h5py. I'm using python v3.7.
@marzamKI try to uninstall numpy and h5py and then do:pip install h5py==2.10.0 pip install numpy==1.19.5In my case, when I run solo jsonfile.json dataset.loom again, I don't have the
TypeError: Indexing arrays must have integeranymore, solo finish preprocessing of the data and start training of the neural network.
It seems to be an issue of h5py/numpy, see here.Best,
Carlo
Hi! I had the same issue and this worked for me. Thanks!
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njbernstein
commented on August 14, 2024
@davek44 can you close this out?
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