Hello,

I'm trying to use ioniser with the function readFast5Summary  but a message error appears:

fast5files <- list.files(path = "/home/ferrato/Documents/fast5", pattern = ".fast5$",full.names = TRUE)

example.summary <- readFast5Summary(fast5files)

Answer:

Checking file validity
Reading Channel Data
Reading Raw Data
Reading Template Data
Reading Complement Data
Reading Template FASTQ
Error in .subset(x, j) : type 'closure' d'indice incorrect

Could you say me what to do please ?

Lionel

For the files:

https://drive.google.com/drive/folders/0B-dW0jY0Jr0COVNsTzlmYkRNSWs

Here you are the output of sessionInfo():

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
[1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C            
[3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8  
[5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8 
[7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C               
[9] LC_ADDRESS=C               LC_TELEPHONE=C          
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base     

other attached packages:
[1] IONiseR_1.0.1        BiocInstaller_1.20.3 gridExtra_2.2.1   
[4] ggplot2_2.2.1        poRe_0.21            svDialogs_0.9-57  
[7] svGUI_0.9-55         data.table_1.10.4    shiny_1.0.0       
[10] bit64_0.9-5          bit_1.1-12           rhdf5_2.14.0        

loaded via a namespace (and not attached):
[1] Rcpp_0.12.9                RColorBrewer_1.1-2      
[3] futile.logger_1.4.3        plyr_1.8.4              
[5] GenomeInfoDb_1.6.3         XVector_0.10.0          
[7] futile.options_1.0.0       bitops_1.0-6            
[9] tools_3.2.3                zlibbioc_1.16.0         
[11] digest_0.6.12              lattice_0.20-34         
[13] tibble_1.2                 gtable_0.2.0            
[15] DBI_0.5-1                  dplyr_0.5.0             
[17] hwriter_1.3.2              Biostrings_2.38.4       
[19] S4Vectors_0.8.11           IRanges_2.4.8           
[21] stats4_3.2.3               grid_3.2.3              
[23] Biobase_2.30.0             R6_2.2.0                
[25] BiocParallel_1.4.3         latticeExtra_0.6-28     
[27] tidyr_0.6.1                magrittr_1.5            
[29] lambda.r_1.1.9             scales_0.4.1            
[31] Rsamtools_1.22.0           htmltools_0.3.5         
[33] BiocGenerics_0.16.1        GenomicRanges_1.22.4    
[35] GenomicAlignments_1.6.3    ShortRead_1.28.0        
[37] assertthat_0.1             SummarizedExperiment_1.0.2
[39] mime_0.5                   xtable_1.8-2            
[41] colorspace_1.3-2           httpuv_1.3.3            
[43] lazyeval_0.2.0             munsell_0.4.3           
> example.summary <- readFast5Summary(fast5files[1])
Checking file validity
Reading Channel Data
Reading Raw Data
Reading Template Data

Thank you for providing the files.  These currently haven't been based-called, the only data in there is the raw-signal.  You're using an older version of R and IONiseR (R is now on version 3.3.2), and at the time the version you're using was written it wasn't possible to produce fast5 files like this - hence the unhelpful error message.

If you use the developmental version of the package here, you will atleast get an message informing you what's happened.

> readFast5Summary(files)
Checking file validity
Reading Channel Data
Error in readFast5Summary(files) : 
  No files matched the expected fast5 file structure.
  Have they been processed and basecalled with MinKNOW?

Given the names of your files, I would guess these were generated during the initial mux scan, when you're setting up the device, rather than a live sequencing run.  If that is the case, it probably explains why no base calling as been done.  If this is real data, then I would suggest you use Oxford Nanopore's tools to carry out base calling, before trying to use IONiseR to look at the data.

Thank you very much.

It was a version problem.

Now all works fine.