search

Fraternalilab / sciCSR

Single-Cell Inference of Class Switch Recombination
GNU General Public License v3.0
18 stars 3 forks source link

scipy.sparse.linalg._eigen.arpack.arpack.ArpackError #2

Closed WhaleGe closed 12 months ago

WhaleGe commented 12 months ago

Thank you very much for the tool you developed. It can help everyone save more time to study B cells. However, when I use it to run my own data, it keeps reporting errors. The following is the specific information of the error. Thank you very much for taking the time to look at this issue.

g_r_csr <- fitTransitionModel( anndata_file = "obj_sampled_bcells_assay-RNA_R.h5ad", mode = "pseudotime", pseudotime_key = "csr_pot" ) 100%|██████████████████████████████████████████████████████████████████████████████| 6778/6778 [00:06<00:00, 1003.81cell/s] Error in py_call_impl(callable, dots$args, dots$keywords) : scipy.sparse.linalg._eigen.arpack.arpack.ArpackNoConvergence: ARPACK error -1: No convergence (67781 iterations, 11/20 eigenvectors converged) g_r_shm <- fitTransitionModel(l( anndata_file = "obj_sampled_bcells_assay-RNA_R.h5ad", mode = "pseudotime", pseudotime_key = "shm" ) 100%|██████████████████████████████████████████████████████████████████████████████| 6778/6778 [00:06<00:00, 1084.79cell/s] Error in py_call_impl(callable, dots$args, dots$keywords) : scipy.sparse.linalg._eigen.arpack.arpack.ArpackError: ARPACK error 3: No shifts could be applied during a cycle of the Implicitly restarted Arnoldi iteration. One possibility is to increase the size of NCV relative to NEV.

WhaleGe commented 12 months ago

I have solved it. It may be caused by the inconsistent number of cells in the two assays.