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digitalcytometry / cytospace

CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
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Illegal hardware instruction cytospace -sp -ctp -stp -cp -o -op #102

Open ankushs0128 opened 3 months ago

ankushs0128 commented 3 months ago

Hi,

i am trying to run Cytospace on spatial transcriptomics on Count matrices encountering the illegal hardware instruction. Iam running cytospace on Macos M3 Max Chip. highly appreciate any help in rectifying the error 

Read and validate data ...
100% |██████████████████████████████████████████████████| Reading data [done]
Estimating cell type fractions
2024-06-12 10:53:33 Load ST data
2024-06-12 10:53:52 Load scRNA data
Warning: Invalid name supplied, making object name syntactically valid. New object name is Cell.IDsCellType; see ?make.names for more details on syntax validity
2024-06-12 10:56:14 Integration 
Performing PCA on the provided reference using 1949 features as input.
Projecting PCA
Finding neighborhoods
Finding anchors
    Found 1586 anchors
Filtering anchors
    Retained 1268 anchors
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Predicting cell labels
100% |██████████████████████████████████████████████████| Reading data [done]
Time to read and validate data: 205.86 seconds
Estimating number of cells in each spot ...
Time to estimate number of cells per spot: 0.6 seconds
Down/up sample of scRNA-seq data according to estimated cell type fractions
Time to down/up sample scRNA-seq data: 49.44 seconds
Building cost matrix ...
Time to build cost matrix: 2.08 seconds
Solving linear assignment problem ...
zsh: illegal hardware instruction  cytospace -sp  -ctp  -stp  -cp  -o  -op SampleName1
erinlbrown commented 3 months ago

Hi, thank you for your interest in CytoSPACE! It sounds like there is an incompatibility between the solver and the M3 Max. Could you please share whether you were using the default solver (no additional arguments) or the lap_CSPR solver (-sm lap_CSPR)?

ankushs0128 commented 3 months ago

Hi,

I ran with default commands so no additional arguments on M3 MAX Mac OS. However, 2,3 GHz Quad-Core Intel Core i5 , it seems to be running well.

Looking forward for pointers to rectify the error on M3 Machine