search

GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
384 stars 137 forks source link

Error in ArchRProject #603

Closed tianchen2019 closed 3 years ago

tianchen2019 commented 3 years ago

Attach your log file ArchR-createArrows-2297bbfbc3ce-Date-2021-03-08_Time-15-58-25.log

Describe the bug when i use your tutorial hematopoiesis dataset,the program stops automatically in ArchRProject. the code is 

library(ArchR)
inputFiles <- getTutorialData("Hematopoiesis")
addArchRGenome("hg19")
addArchRThreads(threads = 20)
ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  filterTSS = 4, #Dont set this too high because you can always increase later
  filterFrags = 1000,
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)
ArrowFiles
proj <- ArchRProject(
  ArrowFiles = ArrowFiles,
  outputDirectory = "HemeTutorial",
  copyArrows = TRUE #This is recommened so that you maintain an unaltered copy for later usage.
)

the log file is 

2021-03-08 16:01:41 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding GeneScoreMatrix!, 3.274 mins elapsed.
2021-03-08 16:01:48 : (scATAC_PBMC_R1 : 3 of 3) Adding GeneScoreMatrix!, 3.384 mins elapsed.
2021-03-08 16:02:14 : (scATAC_BMMC_R1 : 1 of 3) Adding GeneScoreMatrix!, 3.821 mins elapsed.
2021-03-08 16:02:21 : (scATAC_CD34_BMMC_R1 : 2 of 3) Finished Creating Arrow File, 3.929 mins elapsed.
2021-03-08 16:02:34 : (scATAC_PBMC_R1 : 3 of 3) Finished Creating Arrow File, 4.149 mins elapsed.
2021-03-08 16:02:55 : (scATAC_BMMC_R1 : 1 of 3) Finished Creating Arrow File, 4.495 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-createArrows-2297bbfbc3ce-Date-2021-03-08_Time-15-58-25.log
[1] "scATAC_BMMC_R1.arrow"      "scATAC_CD34_BMMC_R1.arrow"
[3] "scATAC_PBMC_R1.arrow"
Using GeneAnnotation set by addArchRGenome(Hg19)!
Using GeneAnnotation set by addArchRGenome(Hg19)!
Validating Arrows...

The program seems to stop in Validating Arrows. And the output file HemeTutorial is empty. There is 8.7T of storage left.

rcorces commented 3 years ago

Sorry you are having trouble with running the tutorial. Unfortunately, I am not sure how to help. Creation of Arrow files for the tutorial could take ~10 minutes. Many users have run this tutorial code on the tutorial data across a wide array of computational environments. If you are having trouble, I'd suggest trying a different compute environment in case that is something odd about the one you are using.

tianchen2019 commented 3 years ago

Sorry you are having trouble with running the tutorial. Unfortunately, I am not sure how to help. Creation of Arrow files for the tutorial could take ~10 minutes. Many users have run this tutorial code on the tutorial data across a wide array of computational environments. If you are having trouble, I'd suggest trying a different compute environment in case that is something odd about the one you are using.

After trying, this error has now appeared in this step.

Using GeneAnnotation set by addArchRGenome(Mm10)!
Using GeneAnnotation set by addArchRGenome(Mm10)!
Validating Arrows...
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) :
  HDF5. File accessibilty. Unable to open file.
rcorces commented 3 years ago

From your last post, it looks like you are not running the tutorial code on the tutorial data (you are in mm10). Please run the tutorial code on the tutorial data and report back.

tianchen2019 commented 3 years ago

From your last post, it looks like you are not running the tutorial code on the tutorial data (you are in mm10). Please run the tutorial code on the tutorial data and report back. I found the same error in issues section and solved it with his solution by seting environment variable RHDF5_USE_FILE_LOCKING=FALSE. https://github.com/GreenleafLab/ArchR/issues/248#issuecomment-789453997

rcorces commented 3 years ago

Glad this worked for you. Closing this issue.