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MaayanLab / archs4

ARCHS4 RNA-seq processing scripts and web server pages.
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Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File accessibilty. Unable to open file. #18

Closed Waelali-code closed 3 years ago

Waelali-code commented 4 years ago

I downloaded the R code about human esophagus from https://amp.pharm.mssm.edu/archs4/data.html , and ran on R.

an error was occurred on the step of retrieving information from compressed data,

samples = h5read(destination_file, "meta/Sample_geo_accession") Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File accessibilty. Unable to open file.

this problem has been shared here by others, but I could not solve my problem when I applied the suggested solution, because I am new in using R, please anyone can guide me through this problem, thanks a lot

lachmann12 commented 3 years ago

It could be due to an incomplete or corrupted file download. What is the md5 checksum of the file you downloaded? It should be: 1335b3c972d7038429aa2d36563f61a2 for human_matrix.h5 28c091161fcaeb844b2143e3bbe42243 for mouse_matrix.h5

lachmann12 commented 2 years ago

In case of this error i would recommend a manual download from the archs4 download section. The checksum changed since the last issue. Also the meta data structure has been slightly modified as meta/sample/xxx and meta/gene/xxx