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Error: addGroupCoverages #2315
Description
Hi,
I'm new to handling scATAC-seq data and followed the ArchR tutorial with test data (i.e., Hematopoiesis dataset). When I ran the addGroupCoverages functions for Pseudo-bulk Replicates, there came below error:
projHeme4 <- addGroupCoverages(ArchRProj = projHeme3, groupBy = "Clusters2")
ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-7efb5c5225a6-Date-2025-12-01_Time-11-55-38.417641.log
If there is an issue, please report to github with logFile!
subThreading Enabled since ArchRLocking is FALSE see `addArchRLocking`
2025-12-01 11:55:39.507496 : Creating Coverage Files!, 0.018 mins elapsed.
2025-12-01 11:55:39.507947 : Batch Execution w/ safelapply!, 0.018 mins elapsed.
> #### step 7: pseudo-bulk replicates and peak calling
> ##pseudo-bulk replicates
> projHeme4 <- addGroupCoverages(ArchRProj = projHeme3, groupBy = "Clusters2")
ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-7efb1525e4a4-Date-2025-12-01_Time-11-56-04.961457.log
If there is an issue, please report to github with logFile!
subThreading Enabled since ArchRLocking is FALSE see `addArchRLocking`
2025-12-01 11:56:06.106228 : Creating Coverage Files!, 0.019 mins elapsed.
2025-12-01 11:56:06.10677 : Batch Execution w/ safelapply!, 0.019 mins elapsed.
2025-12-01 11:57:29.098289 : Adding Kmer Bias to Coverage Files!, 1.402 mins elapsed.
Error in .safelapply(seq_along(availableChr), function(x) { :
Error Found Iteration 1 :
[1] "Error in BSgenome[[availableChr[x]]] : no such sequence\n"
<simpleError in BSgenome[[availableChr[x]]]: no such sequence>
Error Found Iteration 2 :
[1] "Error in BSgenome[[availableChr[x]]] : no such sequence\n"
<simpleError in BSgenome[[availableChr[x]]]: no such sequence>
Error Found Iteration 3 :
[1] "Error in BSgenome[[availableChr[x]]] : no such sequence\n"
<simpleError in BSgenome[[availableChr[x]]]: no such sequence>
Error Found Iteration 4 :
[1] "Error in BSgenome[[availableChr[x]]] : no such sequence\n"
<simpleError in BSgenome[[availableChr[x]]]: no such sequence>
Error Found Iteration 5 :
[1] "Error in BSgenome[[availableChr[x]]] : no such sequence\n"
<simpleError in BSgenome[[availableChr[x]]]: no such sequence>
Error Found Iteration 6 :
[1] "Error in BSgenome[[availableChr[x]]] : no such sequence\n"
<simpleError in BSgenome[[availableChr[x]]]: no such sequence>
Error Found Iteration 7 :
[1] "Error in BSgenome[[av
In addition: Warning message:
In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) :
24 function calls resulted in an error
log file
ArchR-addGroupCoverages-7efb1525e4a4-Date-2025-12-01_Time-11-56-04.961457.log
ArchR-addGroupCoverages-7efb5c5225a6-Date-2025-12-01_Time-11-55-38.417641.log
ArchR-addGroupCoverages-7efb132cb5c7-Date-2025-12-01_Time-11-46-55.485477.log
Additional context
ArchR version: 1.0.3
Thanks!
Activity
immanuelazn commentedon Dec 1, 2025
Hi @zeyan-0717! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.