Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File accessibilty. Unable to open file.
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2.0 years ago

Hi, I am using the Kallisto-Sleuth pipeline for differential expression of RNA-seq and I am having a problem with performing 'sleuth_prep' in Sleuth. It's my first time to use R package Sleuth, I dont know how solve the problem, any help would be fantastic for me!

t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
"external_gene_name"), mart = mart)
t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id,
ens_gene = ensembl_gene_id, ext_gene = external_gene_name)
library(sleuth)
so <- sleuth_prep(s2c, ~ condition, target_mapping = t2g, extra_bootstrap_summary = TRUE)
reading in kallisto results
dropping unused factor levels
.....
normalizing est_counts
26768 targets passed the filter
normalizing tpm
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) :
HDF5. File accessibilty. Unable to open file.
Warning message:
In check_target_mapping(tmp_names, target_mapping, !is.null(aggregation_column)) :
intersection between target_id from kallisto runs and the target_mapping is empty. attempted to fix problem by removing .N from target_id, then merging back into target_mapping. please check obj\$target_mapping to ensure this new mapping is correct.

kallisto RNA-Seq biomaRt sleuth software error • 3.5k views
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@Kevin Blighe Thanks for your help

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I don't think that there has ever been a clear solution to this problem. It has been documented already, though. - see my comment on Bioconductor, with links to potential solutions: https://support.bioconductor.org/p/130419/#130424

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I am having the same problem. I have tried to figure out how to implement the workarounds, but I am creating the files running jobs on a cluster and 1. the versions listed aren't available and 2. I am just not quite at the level where I can create environments when I run a job, unless that just means setting the modules, in which case I could but the versions don't match the suggested ones...

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Hey Jocelyn, can you possibly elaborate on the pipeline that you are trying to follow? - give program and OS versions, where possible.

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Based on what I read re: this exact error, it was not the code I was running but the system I was running kalliso on when the h5 files were created

Yep, that's the conclusion that I got, too. The error has been reported a few times, as you mention, but no definitive solution or exact diagnosis.

This was my solution, which Ive now had to use twice on 2 different systems:

I did have an exchange with the rhdf5 R package developer, and he managed to solve an issue causing this error for one user, but it wasn't a panacea / global cure

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2.0 years ago

Just use the path of folder with h5 file, and use the kallisto output file without modification of the file name, it works well

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Can you please be more specific?; and show exact commands, where necessary? Some of the issues to which I linked do not relate to Sleuth, so, may not actually be the same error.