GreenleafLab
Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : HDF5. File accessibility. Unable to open file.
while using ArchR pakage i have face this problem for both mm10 anf toturial hg19 datasets. i have unable the multithreading creat my arrow files while using this subThreading = FALSE # Disable multithreading. is there anyone who have good suggestion for me to fix this problem. i have install library for hdf5 and LOLA too but still have this problem. Merged.proj2 <- addArchRAnnotations(ArchRProj = Merged.proj2, db = "LOLA", collection = "EncodeTFBS") ArchR logging to : ArchRLogs/ArchR-addArchRAnnotations-1aaf5561d22cf4-Date-2024-12-05_Time-15-38-16.670967.log If there is an issue, please report to github with logFile! Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : HDF5. File accessibility. Unable to open file.
Hi @IqRaZaFaR16! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
while im using latest version of seurat and seurat object i got an error related to mentioned #2212 thats why i have changed Seurat and SeuratObject version into "Seurat_4.3.0.tar.gz" and "SeuratObject_4.1.3.tar.gz" My current R version
R.version _ platform x86_64-conda-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 4 minor 4.1 year 2024 month 06 day 14 svn rev 86737 language R version.string R version 4.4.1 (2024-06-14) nickname Race for Your Life
BiocManager::version() [1] ‘3.20’
Hi @IqRaZaFaR16 , have you tried from scratch with new h5 files, and new arrow files entirely? Have you also tried creating the ArchR project with copyArrows = FALSE?
Just confirming, is this broken for you when running the tutorial at all, or specific to this ArchR project? It would be good for us to narrow down if this is an environment and data problem, or a code problem. Uploading your ArchR log would also be really helpful. Thanks!
ArchR-addMotifAnnotations-1e0814768ecfe3-Date-2024-12-07_Time-14-59-12.910763.log i have generate these file via using threading=1 Merged.proj2 <- addArchRAnnotations(ArchRProj = Merged.proj2, db = "LOLA",collection = "EncodeTFBS") ArchR logging to : ArchRLogs/ArchR-addArchRAnnotations-1e08147a201e33-Date-2024-12-07_Time-15-14-21.19548.log If there is an issue, please report to github with logFile! Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : HDF5. File accessibility. Unable to open file ###try to resolve this
List available collections in LOLA
listAvailableCollections(db = "LOLA") Error in listAvailableCollections(db = "LOLA") : could not find function "listAvailableCollections" #####also try it with downloaded https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/LOLA-Mm10-v1.Anno then its works Merged.proj2 <- addArchRAnnotations(ArchRProj = Merged.proj2, db = "/home/data/iqra/scATAC-seq_scRNA_seq/Allcell.202009.wodoublet.filtering/Annotations/LOLA-Mm10-v1.Anno" , collection = "EncodeTFBS") ArchR logging to : ArchRLogs/ArchR-addArchRAnnotations-1e08143c427625-Date-2024-12-07_Time-16-44-14.402248.log If there is an issue, please report to github with logFile! 2024-12-07 16:44:14.52332 : Annotating Chromosomes 2024-12-07 16:44:14.524287 : Annotating Chr: chr1 2024-12-07 16:44:14.659356 : Annotating Chr: chr2 2024-12-07 16:44:14.799196 : Annotating Chr: chr3 2024-12-07 16:44:14.903275 : Annotating Chr: chr4 2024-12-07 16:44:15.023331 : Annotating Chr: chr5 2024-12-07 16:44:15.142085 : Annotating Chr: chr6 2024-12-07 16:44:15.247485 : Annotating Chr: chr7 2024-12-07 16:44:15.371012 : Annotating Chr: chr8 2024-12-07 16:44:15.477671 : Annotating Chr: chr9 2024-12-07 16:44:15.589678 : Annotating Chr: chr10 2024-12-07 16:44:15.701171 : Annotating Chr: chr11 2024-12-07 16:44:15.833381 : Annotating Chr: chr12 2024-12-07 16:44:15.924924 : Annotating Chr: chr13 2024-12-07 16:44:16.015618 : Annotating Chr: chr14 2024-12-07 16:44:16.105262 : Annotating Chr: chr15 2024-12-07 16:44:16.202925 : Annotating Chr: chr16 2024-12-07 16:44:16.287265 : Annotating Chr: chr17 2024-12-07 16:44:16.395667 : Annotating Chr: chr18 2024-12-07 16:44:16.47782 : Annotating Chr: chr19 2024-12-07 16:44:16.565611 : Annotating Chr: chrX 2024-12-07 16:44:16.868803 : Annotating Chr: chrY 2024-12-07 16:44:17.518742 : All Regions Overlap at least 1 peak!, 0.052 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-addArchRAnnotations-1e08143c427625-Date-2024-12-07_Time-16-44-14.402248.log