Bug report: cell-type-wilms-tumor-06 - prepare-fetal-references.R - zellkonverter::readH5AD

[maud-p]

Summary

Dear Childhood Cancer Data Lab,

I am back in the analysis of the Wilms tumor 06 dataset and just wanted to re-run the entire workflow 00_run_workflow.sh.

It seems that I have a bug running prepare-fetal-references.R line 138 sce_kidney <- zellkonverter::readH5AD(opts$kidney_ref_file, raw = TRUE).

I get the error Error in lock(plock, exclusive = FALSE) : Cannot open lock file: Permission denied

Code or step

• I forked and cloned the current [OpenScPCA-analysis](https://github.com/AlexsLemonade/OpenScPCA-analysis) directory.
• I downloaded the Wilms tumor 06 data using download-data.py --projects SCPCP000006
• I re-builded the docker (podman) image using podman buildx build . -t openscpca/cell-type-wilms-tumor-06
• In the container, RStudio Terminal, I tried to run the workflow 00_run_workflow.sh

PS: I wasn't sure how to run it directly from my Terminal (MobaXterm).

Desired outcome

get the workflow running and the updated annotation table. I then would like to play with some parameters to see how it affects the annotations.

Observed outcome or error message

I get the following message:
`Loading required package: SeuratObject
Loading required package: sp
‘SeuratObject’ was built under R 4.4.0 but the current version is
4.4.1; it is recomended that you reinstall ‘SeuratObject’ as the ABI
for R may have changed

Attaching package: ‘SeuratObject’

The following objects are masked from ‘package:base’:

intersect, t

Registered S3 method overwritten by 'SeuratDisk':
method from
as.sparse.H5Group Seurat

Attaching shinyBS
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object is masked from 'package:SeuratObject':

intersect

The following objects are masked from 'package:stats':

IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

findMatches

The following objects are masked from 'package:base':

expand.grid, I, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:sp':

%over%

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

rowMedians

The following objects are masked from 'package:matrixStats':

anyMissing, rowMedians

Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:Seurat':

Assays

The following object is masked from 'package:SeuratObject':

Assays

Error in lock(plock, exclusive = FALSE) :
Cannot open lock file: Permission denied
Calls: ... installConda -> lockExternalDir -> lockDirectory -> lock
Execution halted`

Example

I run the different step separatly and I thing the bug comes from the script prepare-fetal-references.R line 138 sce_kidney <- zellkonverter::readH5AD(opts$kidney_ref_file, raw = TRUE).

I tried to use Seurat to open the h5ad file SeuratDisk::LoadH5Seurat(opts$kidney_ref_file) but it did help and I got the error:
Validating h5Seurat file Error: Invalid h5Seurat file: cannot find attribute 'version'

I am not familiar with zellkonverter. Do you have any idea?

Thank you!

[jaclyn-taroni]

Hi @maud-p - Happy New Year, and very glad to see you return to the project! 😄 I am sorry to hear that you've run into an issue. Pinging @jashapiro and @allyhawkins, who I know have worked with zellkonverter before, with the hopes that they can comment on if it's a known issue with a quick fix.

[maud-p]

Thank you! Happy New Year to all of you! 🥳

[allyhawkins]

Looking at what you posted, I don't have an obvious solution, but I will look into it and comment if I find anything!

[jashapiro]

I don't have a quick fix either: My guess is that it is something to do with podman permissions conflicting with something that zellkonverter needs, most likely via the conda system that zellkonverter uses under the hood.

[maud-p]

Just for info, I now switch to another machine which allows the use of Docker and the problem was still persistent.

[jashapiro]

Hi @maud-p: I did some investigating, and I think that the issue is partly in how we set up zellkonverter so that in performs its extra installation steps. Essentially, we set things up so that the root user has all the files they need, but the rstudio user that you are logged in as when using the interactive display does not have all the permissions required by default.

To get around this, you should be able to launch the container with one more environment variable. Add the following option to your launch command: -e ROOT=TRUE

Then you should be able to run sudo bash 00_run_workflow.sh, which should get around the file permission issue.

I don't think this is a permanent solution, but hopefully it will work for what you need now. We may need to modify how we create the Dockerfile to improve this for the future.

[maud-p]

Thank you so much, it seems that it worked 🥳
I'll open a small PR to update the ReadMe.md file!