R command worked yesterday, but stalls today?
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Entering edit mode
29 days ago
cthangav ▴ 10

Hi, I am having trouble with this MOFA Tutorial in R: https://raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/10x_scRNA_scATAC.html

Yesterday, the commands were working but today R stalled on this particular command:

seurat <- seurat %>%
.[,seurat@meta.data$pass_accQC==TRUE & seurat@meta.data$pass_rnaQC==TRUE]


I tried to redo the run but now it keeps stalling on the following command, which is to download the data:

seurat <- readRDS(url("ftp://ftp.ebi.ac.uk/pub/databases/mofa/10x_rna_atac_vignette/seurat.rds"))


R studio displays the red octagonal symbol at the top right corner, indicating it is running the code, but never completes the command. Both commands were working fine yesterday but I haven't been able to get it to work today or figure out what the issue is yet. Do you have any suggestions?

R • 386 views
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29 days ago
Mensur Dlakic ★ 11k

This is like asking us why your soufflé turned out great yesterday but collapsed miserably today. How can we know the answer? Did you do everything the same today compared to yesterday?

But here, since you are asking: network problems, issues with Seurat download site, your computer running other programs in the background or for some reason having less resources available compared to yesterday.

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Entering edit mode
28 days ago
ATpoint 49k

Make it simple and download that RDS file from command line with something like wget, this will give a status bar. Once downloaded just read it in with readRDS, this is probably a matter of slow internet connection in your case why it takes a long time, as suggested in the other answer. It is in fact a 2.5G file so it might take time depending on your connection.

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...besides, wget has a -c/--continue option to resume the download of a partial file without restarting from start.

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Entering edit mode

I think it was an internet issue, thank you for your response!