Index error in the normalization step

[ahalxq]

Hi,

I got an error "IndexError: Unknown indexer True of type <class 'numpy.bool_'>" with the following traceback:
Traceback (most recent call last):
File "3DVI/scripts/3DVI.py", line 373, in
res = [normalize(bandM, cellInfo, chromSelect, bandDist, nLatent, batchFlag, gpuFlag) for bandM, chromSelect, bandDist in bandMiter]
File "3DVI/scripts/3DVI.py", line 373, in
res = [normalize(bandM, cellInfo, chromSelect, bandDist, nLatent, batchFlag, gpuFlag) for bandM, chromSelect, bandDist in bandMiter]
File "3DVI/scripts/3DVI.py", line 157, in normalize
scvi.data.setup_anndata(adata)
File ".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/scvi/data/_anndata.py", line 191, in setup_anndata
local_l_mean_key, local_l_var_key = _setup_library_size(adata, batch_key, layer)
File ".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/scvi/data/_anndata.py", line 807, in _setup_library_size
_compute_library_size_batch(
File ".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/scvi/data/_utils.py", line 73, in _compute_library_size_batch
data = adata[idx_batch].X
File ".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/anndata/_core/anndata.py", line 1108, in getitem
oidx, vidx = self._normalize_indices(index)
File ".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/anndata/_core/anndata.py", line 1089, in _normalize_indices
return _normalize_indices(index, self.obs_names, self.var_names)
File ".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/anndata/_core/index.py", line 35, in _normalize_indices
ax0 = _normalize_index(ax0, names0)
File ".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/anndata/_core/index.py", line 107, in _normalize_index
raise IndexError(f"Unknown indexer {indexer!r} of type {type(indexer)}")

I have no idea what could cause the error. The command I use is:
python 3DVI/scripts/3DVI.py
-b "${bandMax}"
-c "${chrom}"
-r "${resolution}"
-i "${inputDir}"
-o "${outputDir}"
-g "${genomeSize}"
-n 100 -p "${cpuN}"
Could you please help me with it? Thanks a lot!

[yezhengSTAT]

Hello,
Were you able to run the demo data using the commands in step 3? I also did not see these errors before.

[ahalxq]

Hi Ye,

Thanks a lot for your timely response! Yes, I am able to run the demo data with no error. The problem I am facing now is trying to use 3DVI+ for our own single-cell HiC data. If possible, could you please help me with it?

The input file looks like this:
chr10 70000 chr10 70000 69
chr10 70000 chr10 80000 3
chr10 70000 chr10 90000 1
chr10 70000 chr10 100000 4
chr10 70000 chr10 110000 4

Before running 3DVI+, I concatenated the data files for all chromosomes together, and, since there is only 1 dataset, I did not input the cell summary. Could this be the problem?

Here is the program output before running into this error:
Maximum genomic distance: 10
Chromosomes to be processed: chr20
Resolution: 1000000
Path to the input scHi-C data: ../data/Astro/
Path to output directory: ../output/Astro_contact_matrix/
Cell summary file: None
Genome size file: ...//hg19.chrom.sizes
Remove batch effect or not: False
Dimension of latent space: 100
Use GPU or not: False
Number of CPUs for parallel computing: 1
PCA number: 10
UMAP plot: True
t-SNE plot: True
Caculate total number of bin per chromosome.
Prepare cell summary file.
Read in scHi-C data.
Convert interactions into band matrix.
100%|████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 2.22it/s]
Concat cells into cell x locus-pair matrix.
3DVI normalization.
INFO No batch_key inputted, assuming all cells are same batch
.../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/scvi/data/_anndata.py:709: UserWarning: Category 0 in adata.obs['_scvi_batch'] has fewer than 3 cells. SCVI may not train properly.
warnings.warn(
.../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/scvi/data/_anndata.py:716: UserWarning: Is adata.obs['{}'] continuous? SCVI doesn't support continuous obs yet.
warnings.warn(
INFO No label_key inputted, assuming all cells have same label
.../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/scvi/data/_anndata.py:709: UserWarning: Category 0 in adata.obs['_scvi_labels'] has fewer than 3 cells. SCVI may not train properly.
warnings.warn(
INFO Using data from adata.X
INFO Computing library size prior per batch

Thank you so much!

[yezhengSTAT]

Hello,
Glad to hear that the demoData is working!

"I concatenated the data files for all chromosomes together, and, since there is only 1 dataset, I did not input the cell summary."
Do you mean you concatenate all the cells into one file?

".../anaconda3/envs/schic-3dvi/lib/python3.8/site-packages/scvi/data/_anndata.py:709: UserWarning: Category 0 in adata.obs['_scvi_batch'] has fewer than 3 cells. SCVI may not train properly."
Seems that there are fewer than 3 cells are provided?

Please keep all the interactions within each cell in an independent file. You can refer to the demoData folder for reference.

Best,
Ye