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                                            nansne

Could not retrieve index file for .bam

thank you, so i put 'gex_possorted_bam.bam' and 'gex_possorted_bam.bam.bai' into the same folder, and run again, but it failed with ... ![微信图片_20240318154326](https://github.com/single-cell-genetics/cellsnp-lite/assets/161684849/71987660-f523-420e-9a77-5843dcf02622)

runtime and expected output

hello, i ran cellsnp-lite, and it failed with"[E::idx_find_and_load] Could not retrieve index file for '/h/sunnan/VKHDATA/vkha/gex_possorted_bam.bam'", what should i do next? thank you very much!

A large number of cells are unassigned & very few n_vars

Thank you, Yuanhua. The donor VCF had been imputed before. So I followed your second advice, ran cellsnp-lite with the donor VCF, and the code as: cellsnp-lite -s ./gex_possorted_bam.bam -b...

Sparse_Marginsum Error Running IterativeLSI

> The problem occurs when executing this line in my case: > > https://github.com/GreenleafLab/ArchR/blob/d9e741c980c7c64e5348c97a74d146cc95f8ba76/R/AnnotationPeaks.R#L844 > > Basically it looks like yet another problem with the Matrix package since version 1.6-2...