I'm having a bit of trouble running the 'readFAST5Summary' function in IONiseR. The error message mentions HDF5 so I have updated these in the command line using home-brew;
brew install hdf5
pip3 install h5py
and tried to run the code again but it gives me this error message.
> fast5files <- list.files(path = "/Volumes/NGS Lab/MinION/data/downloads/pass/batch_1487083485858", pattern = ".fast5$", full.names = TRUE)
> example.summary <- readFast5Summary( fast5files )
Checking file validity
Reading Channel Data
Reading Raw Data
Reading Template Data
Error in H5Aopen(did, "duration") :
HDF5. Attribute. Unable to initialize object.
I think that I have installed all of the additional packages.
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 BiocStyle_2.2.1 knitr_1.15.1 rmarkdown_1.4 testthat_1.0.2 gridExtra_2.2.1 ggplot2_2.2.1 IONiseR_1.4.4
loaded via a namespace (and not attached):
 Rcpp_0.12.10 RColorBrewer_1.1-2 GenomeInfoDb_1.10.3 plyr_1.8.4
 XVector_0.14.1 bitops_1.0-6 tools_3.3.3 zlibbioc_1.20.0
 digest_0.6.12 evaluate_0.10 tibble_1.2 gtable_0.2.0
 rhdf5_2.18.0 lattice_0.20-35 Matrix_1.2-8 DBI_0.6
 parallel_3.3.3 stringr_1.2.0 hwriter_1.3.2 dplyr_0.5.0
 Biostrings_2.42.1 S4Vectors_0.12.2 IRanges_2.8.2 rprojroot_1.2
 stats4_3.3.3 grid_3.3.3 data.table_1.10.4 Biobase_2.34.0
 R6_2.2.0 BiocParallel_1.8.1 latticeExtra_0.6-28 tidyr_0.6.1
 magrittr_1.5 backports_1.0.5 htmltools_0.3.5 scales_0.4.1
 Rsamtools_1.26.1 GenomicAlignments_1.10.1 BiocGenerics_0.20.0 GenomicRanges_1.26.4
 ShortRead_1.32.1 assertthat_0.1 SummarizedExperiment_1.4.0 colorspace_1.3-2
 stringi_1.1.3 RCurl_1.95-4.8 lazyeval_0.2.0 munsell_0.4.3
Any help to resolve this would be appreciated.
I notice you have a space in the path to your data, which is generally not a good idea. It might be unrelated to this issue (but I would suggest you to test it anyway).