HDF5 error in addGeneIntegrationMatrix

[cschmidl]

Dear Archers,

I run into problems with the function addGeneIntegrationMatrix which gives the following error:

ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-13a493e8b0b4b-Date-2021-01-19_Time-15-14-08.log If there is an issue, please report to github with logFile! 2021-01-19 15:14:08 : Running Seurat's Integration Stuart* et al 2019, 0.001 mins elapsed. 2021-01-19 15:14:09 : Checking ATAC Input, 0.002 mins elapsed. 2021-01-19 15:14:09 : Checking RNA Input, 0.002 mins elapsed. 2021-01-19 15:14:11 : Found 13612 overlapping gene names from gene scores and rna matrix!, 0.039 mins elapsed. 2021-01-19 15:14:11 : Creating Integration Blocks, 0.039 mins elapsed. 2021-01-19 15:14:11 : Prepping Interation Data, 0.04 mins elapsed. Filtering 16 dims correlated > 0.75 to log10(depth + 1) 2021-01-19 15:14:12 : Computing Integration in 2 Integration Blocks!, 0 mins elapsed. 2021-01-19 15:14:12 : Block (1 of 2) : Computing Integration, 0 mins elapsed. 2021-01-19 15:14:12 : Block (1 of 2) : Identifying Variable Genes, 0.002 mins elapsed. 2021-01-19 15:14:12 : Block (1 of 2) : Getting GeneScoreMatrix, 0.009 mins elapsed. 2021-01-19 15:14:34 : Block (1 of 2) : Imputing GeneScoreMatrix, 0.372 mins elapsed. Error in H5Fcreate(file) : HDF5. File accessibilty. Unable to open file.

I set threads already to 1 and also checked the integrity of the ArchRproject with h5ls(getArrowFiles(projCore)[1]), and the file looks fine I think.

Debugging suggests that addImputeWeights could cause the error but I'm just a beginner in R and can't resolve this on my own.

I attached the logfile and would be very happy for help!

Thanks a lot and best wishes ArchR-addGeneIntegrationMatrix-13a493e8b0b4b-Date-2021-01-19_Time-15-14-08.log

[rcorces]

I'm not sure I know how to solve this one. Does this happen with all or your projects or is it just this particular project?

[rcorces]

Closing due to inactivity. Feel free to comment again here and I will re-open if you still need help.