Error splitting archr project

[drighelli]

Hi,

I have an ArchR project where I have six samples of two different conditions, but I'm trying to split the project dividing it by condition.

My idea is to select the cells of each condition and then subsetting the project based on these cells, but when I try to do that it returns me a not so much informative error.

Archrlog.log

I tried the following instruction also with dropCells=FALSE and obtained the same error message.

Thanks in advance.
Dario

proj_WT <- subsetArchRProject(
  ArchRProj = proj,
  cells = cells,
  outputDirectory = "archr_mo_sleep_WT",
  dropCells = TRUE,
  force=TRUE,
  logFile="ArchRLogs/Archrlog.log"
)
Copying ArchRProject to new outputDirectory :  PATH
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 9): Annotations
Copying Other Files (2 of 9): ArchRLogs
Copying Other Files (3 of 9): Embeddings
Copying Other Files (4 of 9): GroupCoverages
Copying Other Files (5 of 9): IterativeLSI
Copying Other Files (6 of 9): PeakCalls
Copying Other Files (7 of 9): Plots
Copying Other Files (8 of 9): Rplots.pdf
Copying Other Files (9 of 9): tmp
Error in saveArchRProject(ArchRProj = ArchRProj[cells, ], outputDirectory = outputDirectory,  : 
  all(file.exists(zfiles)) is not TRUE

Session Info

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
  
Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
  
Random number generation:
 RNG:     L'Ecuyer-CMRG
 Normal:  Inversion
 Sample:  Rejection
  
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  
time zone: Etc/UTC
tzcode source: system (glibc)
  
attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils
 [8] datasets  methods   base
  
other attached packages:
 [1] rhdf5_2.44.0                SummarizedExperiment_1.30.2
 [3] Biobase_2.60.0              MatrixGenerics_1.12.3
 [5] Rcpp_1.0.11                 Matrix_1.6-0
 [7] GenomicRanges_1.52.0        GenomeInfoDb_1.36.1
 [9] IRanges_2.34.1              S4Vectors_0.38.1
[11] BiocGenerics_0.46.0         matrixStats_1.0.0
[13] data.table_1.14.8           stringr_1.5.0
[15] plyr_1.8.8                  magrittr_2.0.3
[17] ggplot2_3.4.2               gtable_0.3.3
[19] gtools_3.9.4                gridExtra_2.3
[21] ArchR_1.0.2
  
loaded via a namespace (and not attached):
 [1] utf8_1.2.3              generics_0.1.3          bitops_1.0-7
 [4] stringi_1.7.12          lattice_0.21-8          fansi_1.0.4
 [7] scales_1.2.1            abind_1.4-5             cli_3.6.1
[10] rlang_1.1.1             crayon_1.5.2            XVector_0.40.0
[13] munsell_0.5.0           withr_2.5.0             DelayedArray_0.26.7
[16] S4Arrays_1.2.0          tools_4.3.1             dplyr_1.1.2
[19] colorspace_2.1-0        Rhdf5lib_1.22.0         GenomeInfoDbData_1.2.10
[22] vctrs_0.6.3             R6_2.5.1                lifecycle_1.0.3
[25] zlibbioc_1.46.0         pkgconfig_2.0.3         pillar_1.9.0
[28] glue_1.6.2              tibble_3.2.1            tidyselect_1.2.0
[31] rhdf5filters_1.12.1     Cairo_1.6-0             c

[rcorces]

Hi @drighelli! 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.

It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably 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.