Error ReadMtx ( Cannot find expression matrix)

[ahmedibatta]

I am trying using the ReadMtx function to single-cell data with different names but I got Cannot find expression matrix

my code:

file_temp = "/data/external/ms/MS19270_PBMC"

mxt_temp= paste0(file_temp,'/',list.files(file_temp,pattern="*_matrix.mtx.gz"))
print(mxt_temp)
cells_temp= paste0(file_temp,'/',list.files(file_temp ,pattern="*_barcodes.tsv.gz"))
print(cells_temp)
features_temp = paste0(file_temp,'/',list.files(file_temp ,pattern="*_genes.tsv.gz"))
print(features_temp)
counts_temp <- ReadMtx(mtx = mxt_temp,cells = cells_temp,features =  features_temp)

the results :

[1] "/data/external/ms/MS19270_PBMC/GSM4104134_MS19270_PBMCs_GRCh38_matrix.mtx.gz"
[1] "/data/external/ms/MS19270_PBMC/GSM4104134_MS19270_PBMCs_GRCh38_barcodes.tsv.gz"
[1] "/data/external/ms/MS19270_PBMC/GSM4104134_MS19270_PBMCs_GRCh38_genes.tsv.gz"
Error: Cannot find expression matrix at /data/external/ms/MS19270_PBMC/GSM4104134_MS19270_PBMCs_GRCh38_matrix.mtx.gz
Traceback:

1. ReadMtx(mtx = mxt_temp, cells = cells_temp, features = features_temp)
2. stop(err, call. = FALSE)

when I checked by list.files(file_temp), the files are present

R session

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=ar_EG.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=ar_EG.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=ar_EG.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=ar_EG.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] patchwork_1.1.1    dplyr_1.0.7        SeuratObject_4.0.2 Seurat_4.0.3      

[saketkc]

Thanks @Ahmed-fub, I confirm this is a bug. We'll have a fix soon.

[andrewwbutler]

This should be fixed now on the develop branch. Please try installing (instructions here) and see if that resolves the issue.

[no-response]

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