RunAzimuth error, Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed

[Cathy94]

Dear Team,

I have successfully executed RunAzimuth with "human_cd34_bone_marrow.h5ad". But when I used my data, it is giving following error:
Running UMAP projection
17:10:40 Read 64830 rows
17:10:40 Processing block 1 of 1
17:10:40 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
17:10:40 Initializing by weighted average of neighbor coordinates using 1 thread
17:10:41 Commencing optimization for 67 epochs, with 1296600 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:11:08 Finished
Warning: No assay specified, setting assay as RNA by default.
Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning messages:
1: In RunUMAP.default(object = neighborlist, reduction.model = reduction.model, :
Number of neighbors between query and reference is not equal to the number of neighbors within reference
2: Cannot add objects with duplicate keys (offending key: UMAP_), setting key to 'ref.umap_'
3: non-unique values when setting 'row.names': ‘CGTCCATAGGAATTAC-1_3’, ‘TCAGGTATCTCTGCTG-1_7’

Could you help me solve this problem? Thank you.

[mihem]

Not a seurat team member. But as the error says you have tuplicate row names, but on the Seurat github channel you'll find several related issue satijalab/seurat#1710

[Cathy94]

Not a seurat team member. But as the error says you have tuplicate row names, but on the Seurat github channel you'll find several related issue satijalab/seurat#1710

Thank you for reply. I tried make.uniqe(), but failed. I think my seurat.obj don't have duplicate row.names. And this could help me: ##138