Error in h5checktypeOrOpenLoc()

[Yiqa]

Hi, thank you for creating this package.
I got Error in h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native): Error in h5checktypeOrOpenLoc(). Cannot open file. File '/data/proj/GCB_FBP/human_dev/exploratory/hca_dev_best3/ArrowFiles/HES1.arrow' does not exist.
Traceback:

1. getPeakMatrix(proj)
2. ArchR::getMatrixFromProject(ArchRProject, useMatrix = "PeakMatrix")
3. getAvailableMatrices(ArchRProj)
4. .availableArrays(getArrowFiles(ArchRProj = ArchRProj))
5. .safelapply(seq_along(ArrowFiles), function(x) {
   . groups <- h5ls(ArrowFiles[x]) %>% {
   . .[.$group == "/" & .$otype == "H5I_GROUP", "name"]
   . }
   . groups <- groups[!grepl("Fragments|Metadata", groups)]
   . groups
   . }, threads = threads) %>% Reduce("intersect", .)
6. Reduce("intersect", .)
7. .safelapply(seq_along(ArrowFiles), function(x) {
   . groups <- h5ls(ArrowFiles[x]) %>% {
   . .[.$group == "/" & .$otype == "H5I_GROUP", "name"]
   . }
   . groups <- groups[!grepl("Fragments|Metadata", groups)]
   . groups
   . }, threads = threads)
8. lapply(...)
9. FUN(X[[i]], ...)
10. h5ls(ArrowFiles[x]) %>% {
    . .[.$group == "/" & .$otype == "H5I_GROUP", "name"]
    . }
11. h5ls(ArrowFiles[x])
12. h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native)
13. stop("Error in ", fctname, ". Cannot open file. File '", file,
    . "' does not exist.")

Could you help me with this?

[rootze]

@Yiqa Thanks for using ArchRtoSignac. I'm not sure which function you are running? More information, including what you run and provided in that function would be better for me to understand what could potentially cause the error. Thank you!

[Yiqa]

Hi, thank you for your reply, sorry for unclear question.

When I run the step to obtain ArchRProject peak matrix for object conversion.

proj <- readRDS("home/private/archr_proj.rds")
pkm <- getPeakMatrix(proj)

I got the error as shown in the above conversation

[rootze]

proj <- readRDS("home/private/archr_proj.rds")

Hello @Yiqa

Did you call peakMatrix in your ArchRProject?
Please run the following code and let me know. I wonder what matrix you have in your data.

getAvailableMatrices(proj)

If you don't have a peak matrix in your ArchRProject, you have to proceed to the step calling-peaks-with-archr https://www.archrproject.com/bookdown/calling-peaks-with-archr.html

ArchR handles the peak calling approach and stores the data differently than Signac, and we argued that you need to finish the peak calling steps before successfully transferring it to Signac.

[Yiqa]

@rootze Hi, sorry for late reply.
When I run getAvailableMatrices(proj)

I get an error:
Error in h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native): Error in h5checktypeOrOpenLoc(). Cannot open file. File '/data/proj/GCB_FBP/human_dev/exploratory/hca_dev_best3/ArrowFiles/HES1.arrow' does not exist.

It seems that I don't have a peak martix in my ArchRProject, I am a bit new to use ArchR, thank you for your guidance, I will try your suggestions.

[rootze]

When I run getAvailableMatrices(proj)

I get an error: Error in h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native): Error in h5checktypeOrOpenLoc(). Cannot open file. File '/data/proj/GCB_FBP/human_dev/exploratory/hca_dev_best3/ArrowFiles/HES1.arrow' does not exist.

Hello @Yiqa
I suspected that your ArchRProject has no peak matrix. But by running a function from ArchR package getAvailableMatrices(proj). This error tells me there is something wrong with your sample arrow file HES1
/data/proj/GCB_FBP/human_dev/exploratory/hca_dev_best3/ArrowFiles/HES1.arrow.

Do all your samples have arrow files beside HES1? You may want to double-check if there are errors when you createArrowFiles. Please let me know. Thank you!

[rootze]

@Yiqa Closed due to GitHub issue inactivity. Feel free to reopen if needed.