Hmmm I think this has happened for some other people. I will look into this sorry for the delay.

I'm assuming that this is related to running on windows. Windows is not supported and its not possible for us to troubleshoot this. I'm closing this issue.

I got the same issue when running in linux.

Can you try running with 1 thread and see if this solves the problem?

Thank you for your answer, but the issue still still exists when I use a thread.

Sorry for the delays @Carota-1.

Can you try with the new release branch. I added more stability and logging and more features --

For Example

#New Release Branch
devtools::install_github("GreenleafLab/ArchR", ref="release_1.0.0", repos = BiocManager::repositories())

library(ArchR)
proj <- getTestProject()

p <- plotTSSEnrichment(ArchRProj = proj, groupBy = "Clusters")
plotPDF(p)

p <- plotFragmentSizes(ArchRProj = proj, groupBy = "Clusters")
plotPDF(p)

Closing due to inactivity. Feel free to post to this thread if the problem can be reproduced with the latest version of ArchR and we will re-open the issue.

Sorry for the delays @Carota-1.

Can you try with the new release branch. I added more stability and logging and more features --

For Example

#New Release Branch
devtools::install_github("GreenleafLab/ArchR", ref="release_1.0.0", repos = BiocManager::repositories())

library(ArchR)
proj <- getTestProject()

p <- plotTSSEnrichment(ArchRProj = proj, groupBy = "Clusters")
plotPDF(p)

p <- plotFragmentSizes(ArchRProj = proj, groupBy = "Clusters")
plotPDF(p)

I got the same issue running on linux and using the 1.0.0 version of ArchR. Also tried 1 thread, it didn't help.

@zhijunyuu - Can you provide a log file?

@zhijunyuu - Can you provide a log file?

ArchR-plotTSSEnrichment-6a771b6c7cfb-Date-2020-12-10_Time-10-49-07.log

Hello all, Thank you for your suggestions. I set the ArchR threads = 16 by running force = TRUE and that worked. Attached is the beautiful new plot! It does look like it's something to do with the threads?

Thanks,
Kaivalya

@Kaivalyamolugu - Thanks for confirming this. You are correct - there is something funky going on when threads = 1 in this function. I can recapitulate this error when I set threads = 1

proj <- getTestProject()
addArchRThreads(threads = 1)
plotTSSEnrichment(ArchRProj = proj, groupBy = "Clusters")

This is calculated incorrectly within the function and (unsurprisingly) when you use returnDF = TRUE the data frame object is incorrect as well:

> df1 <- plotTSSEnrichment(ArchRProj = proj, groupBy = "Clusters", returnDF = TRUE)
> df1[which(df1$x == 0),]
DataFrame with 5 rows and 5 columns
        group         x     value          normValue       smoothValue
  <character> <numeric> <integer>          <numeric>         <numeric>
1          C1         0       918   21.4182240278584  21.0873423732391
2          C2         0         7 0.0694334780892223 0.081156013351039
3          C3         0        21  0.696764608781776 0.811383895074882
4          C4         0        29  0.883315653886953 0.863932551764041
5          C5         0        14   1.37268292682927  1.22115299334812

I havent figured out where the problem is in the code but @jgranja24 will figure it out

Hello again, My R is crashing since I've set the threads to 16. Do you think it would be okay to set the threads to 1 for the rest of the code and set to 16 only for the TSS enrichment plot step?
Thanks,
Kaivalya

@Kaivalyamolugu - according to your logfile, ArchR only really detects 3 cores on your machine. The error with threads = 1 should be limited to plotTSSEnrichment(). Try threads = 2 though. this should be fine on your system.

Thank you for letting me know!

Hello, I am also getting the same problem on my 6 samples. I cannot use any other threads except for threads = 1. I am using macOS.

@sqs1020 - I believe your problem is unrelated. see #1145 (comment)
just run library(parallel) before using ArchR when using threads > 1

@sqs1020 - I believe your problem is unrelated. see #1145 (comment) just run library(parallel) before using ArchR when using threads > 1

Thanks for the reply. My innitial problem is related, that is asscociated with the "plotTSSEnrichment" function (see attached scrreenshot). And then I found this ticket and read the comments. People are saysing using different threads can solve the problem and that's why I have the problem trying different threads. Thank you!

library(parallel)

After using library(parallel) and trying threads = 6 , the problem solved. Thanks again!

This issue has finally been fixed via 506161d in release_1.0.2. It was a C++ bug.