GreenleafLab
Stuck at getImputeWeights(proj) in tutorial
ArchR-plotEmbedding-219fb259eebe8-Date-2024-11-29_Time-22-28-55.260645.log ArchR-plotEmbedding-216108101f6680-Date-2024-11-29_Time-21-17-52.70585.log
Going through the tutorial dataset, in the imputing weights section, things keep getting stuck at the "imputing matrix" stage, couldn't find anything similar in the discussions.
Here is the code that I run:
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", name = markerGenes, embedding = "UMAP", imputeWeights = getImputeWeights(proj) )
And the message that is stuck in the console:
"Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-219fb259eebe8-Date-2024-11-29_Time-22-28-55.260645.log If there is an issue, please report to github with logFile! 2024-11-29 22:28:55.565916 : Getting Matrix Values...
Imputing Matrix"
Looking at the tutorial dataset quick guide and full manual this step should be fairly quick, but I've left it for up to an hour with no change. Has this been noticed before? I couldn't find any clues in the logfile (they show where it gets stick, have a few more that are the same). Usually when there's a missing dependency it's good with flagging it up but that hasn't happened. Any advice would be appreciated!
Hi @mohsinbadat! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
Hi @mohsinbadat, can you confirm that this issue is happening through a fresh docker image as well? You can test this out through the information provided here: https://github.com/GreenleafLab/ArchR/pull/2238/files
Hi @immanuelazn Sorry for not replying, I'm using this on our local cluster and Docker isn't supported, it's been a bit non-trivial trying to test what you said, no luck thus far.
If it helps I've tried using previous versions of ArchR eg 1.0.1 as well as the dev branch, but no luck. If anything springs to mind please do let me know, I just didn't want you to think I'd ignored your advice!