Error in system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE)

[sylestiel]

@rcorces Unfortunately I have encountered the same error: Error in system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE) : error in running command

I have run the addReproduciblePeakSet command numerous times without any issue. Hence, I'm confounded. The log file is attached. Hope you can help me troubleshoot. ArchR-addGroupCoverages-8e7d106fa905-Date-2022-06-21_Time-12-38-45.log

Originally posted by @sylestiel in https://github.com/GreenleafLab/ArchR/issues/200#issuecomment-1162083527

[rcorces]

Hi @sylestiel! 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.
Before we help you, you must respond to the following questions 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. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. 3. Did you post your log file? If not, add it now. 4. 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.

[rcorces]

you've attached a log file for addGroupCoverages() but are reporting an error for addReproduciblePeakSet(). In all likelihood, something has changed on your end if this was working before. It is likely a problem with your macs2 installation.

[sylestiel]

Trying to reinstall ArchR.

Getting the following error

devtools::install_github("GreenleafLab/ArchR", ref="1.0.2", repos = BiocManager::repositories()) Downloading GitHub repo GreenleafLab/ArchR@1.0.2 Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL 'https://api.github.com/repos/GreenleafLab/ArchR/tarball/1.0.2'

[rcorces]

1.0.2 is incorrect. its release_1.0.2

[sylestiel]

You were correct. The problem was with my path to MACS2.

[Larrycpan]

you've attached a log file for addGroupCoverages() but are reporting an error for addReproduciblePeakSet(). In all likelihood, something has changed on your end if this was working before. It is likely a problem with your macs2 installation.

@rcorces I have the same error. I have installed macs2 in my end, and there's no error when I perform macs2 callpeak -h. However, the function addReproduciblePeakSet cannot identify the macs2 application, even though I provide the full path.

proj.CRC <- addReproduciblePeakSet(ArchRProj = proj.CRC,
                                   groupBy = "Clusters",
                                   pathToMacs2 = "/media/xxx/xxx/bin/anaconda3/envs/r4-base/bin/macs2")

Look forward to your reply. ArchR-addGroupCoverages-70c4846c19d2f-Date-2022-08-04_Time-16-55-44.log

[jum1996]

/I have been having the same issue:

`> pathToMacs2 <- findMacs2() Searching For MACS2.. Found with $path!

projHeme4 <- addReproduciblePeakSet(

• ArchRProj = projHeme4,
• groupBy = "Clusters",
• pathToMacs2 = pathToMacs2
• ) Error in system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE) : error in running command`

I am following the tutorial line by line, I also tried specifying the path and same error. Also, it didn't generate a log file