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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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H5 file read error #387

Closed honghh2018 closed 3 years ago

honghh2018 commented 3 years ago

Hi @All, Sorry bother again, I am unable to work well for the ArchR because i am unclear for the really steps for the archr workflow so much. For the step like below, occurred error. 2020-11-02 09:39:20 : Annotating Chr: chr1 Error in H5Fopen(file) : HDF5. File accessibilty. Unable to open file. Calls: addArchRAnnotations ... lapply -> FUN -> .getRegionsFromAnno -> .h5read -> H5Fopen stop executed Even i found the h5 file like '/share/disk1/Data/Users/xiecs/Test/20201026ArchR/Save-ProjHeme4/GroupCoverages/C5..H1.insertions.coverage.h5' but it still get error. which H5 file should the function of archr read ? How could i solve this error ? any help would be appreciated.

jgranja24 commented 3 years ago

Hi @honghh2018, do you mind adding this information to the other issue you already opened https://github.com/GreenleafLab/ArchR/issues/381? It seems related.

honghh2018 commented 3 years ago

Hi @jgranja24 , Thanks for remind me the #381, however the LOLA annotation was already downloaded through your advices using wget command , It had me confuse a lot. the file showing below, had been download a few days ago. /share/nas2/public/R/library/3.6/ArchR/data/Annotations/LOLA-Mm10-v1.Anno The below picture was part of the ArchR directory, image So what wrong for the LOLA files ? Had i done some wrong with the LOLA file downloaded? Any help would be grateful. Best,

rcorces commented 3 years ago

Closing due to inactivity. Feel free to post to this thread if the problem can be reproduced with the latest version of ArchR and we will re-open the issue.

YaoyJiang commented 5 months ago

Hi @jgranja24 , Thanks for remind me the #381, however the LOLA annotation was already downloaded through your advices using wget command , It had me confuse a lot. the file showing below, had been download a few days ago. /share/nas2/public/R/library/3.6/ArchR/data/Annotations/LOLA-Mm10-v1.Anno The below picture was part of the ArchR directory, image So what wrong for the LOLA files ? Had i done some wrong with the LOLA file downloaded? Any help would be grateful. Best,

did you solve this problem? I met the same error