Question: Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File accessibilty. Unable to open file.
0
gravatar for ladavion
5 months ago by
ladavion10
ladavion10 wrote:

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
merging in metadata
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.
ADD COMMENTlink modified 4 months ago by jocelyn.petitto10 • written 5 months ago by ladavion10
1

@Kevin Blighe Thanks for your help

ADD REPLYlink written 5 months ago by ladavion10

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

ADD REPLYlink written 5 months ago by Kevin Blighe66k

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...

ADD REPLYlink written 4 months ago by jocelyn.petitto10

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

ADD REPLYlink written 4 months ago by Kevin Blighe66k

Hello, I was trying to use the pipeline as described in the sleuth documentation for going kallisto->sleuth. I have found the same problem documented a few times re: h5 files in the same process. Right now, I cannot locate the tutorial I was looking to go through it, but as soon as it came to loading the h5 file, I had an issue. Unfortunately, I did not save the code I had used. Generally I run everything in an R Markdown document, but for whatever reason I neglected to that evening and shut RStudio, losing what I was running on the commend line. I believe it used the cowplot data and included a portion re: downloading the information to go from ensembl transcript ids -> gene names. 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. I would assume I was running things on a linux based cluster, but I did not pay that much attention to the node that the jobs were run on. It isn't a thing I knew had any reason to take note of at the time. My own computer is running macOS 10.15.5. I do know that the cluster does not have the latest version of kallisto (I think it is one or two behind whatever environment was set up as a potential solution on one of the git issue threads) and I do not think the same version of the h5 creating library/package/?, but I didn't need to load that module when I used kallisto. I did not know which would work correctly give the version of kallisto I was running (kallisto/0.45.0)

ADD REPLYlink written 3 months ago by jocelyn.petitto10

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

ADD REPLYlink modified 3 months ago • written 3 months ago by Kevin Blighe66k
0
gravatar for ladavion
5 months ago by
ladavion10
ladavion10 wrote:

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

ADD COMMENTlink written 5 months ago by ladavion10

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.

ADD REPLYlink written 5 months ago by Kevin Blighe66k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1395 users visited in the last hour