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Question: Problem with the readFast5Summary command
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gravatar for ferrato
3 months ago by
ferrato0
ferrato0 wrote:

Hello,

I have a problem with my set of fast5 files.

When I run the readFast5Summary command I obtain this message error :

Error opening: shares-net/sequencages/nanopore/fast5/FAD22491_20161011/uploaded/dnacpc14_20161011_FNFAD22491_MN17734_sequencing_run_run2_46863_ch128_read696_strand.fast5 - File Skipped

Reading Channel Data
Error in data.table(id = 1:nrow(readInfo), file = basename(files), readInfo) :
  Item 2 has no length. Provide at least one item (such as NA, NA_integer_ etc) to be repeated to match the 2 rows in the longest column. Or, all columns can be 0 length, for insert()ing rows into.

I have R 3.3.3 and ioniser 1.4.4.

Here you are some files of my dataset:

https://drive.google.com/open?id=0B-dW0jY0Jr0CYWQybF8wWGc2U1k

Can you help me please ?

 

Best regards.

ADD COMMENTlink modified 3 months ago by Mike Smith1.7k • written 3 months ago by ferrato0

Hi,

Thanks for providing the example files.  I'm on holiday at the moment, but I'll take a look at this error when I get back next week.  It's not something I've seen before, so maybe the file format has changed again.

Cheers,

Mike

ADD REPLYlink written 3 months ago by Mike Smith1.7k
0
gravatar for Mike Smith
3 months ago by
Mike Smith1.7k
EMBL Heidelberg / de.NBI
Mike Smith1.7k wrote:

I've tested the package with your files and it seems to work fine.  I suspect the error you're seeing is because the file can't be accessed.  You need to make sure the path to the files is either absolute i.e. starting at the root of your system, or is relative to the current working directory of your R session.  I prefer using absolute paths and if you're following the package vignette, and using list.files() to find all the fast5 files in a folder, you need to set the argument full.names = TRUE e.g.

fast5files <- list.files(path = "/path/to/data/", pattern = ".fast5$", full.names = TRUE)

With your data I get:

> readFast5Summary(fast5files)
Checking file validity
Reading Channel Data
Reading Raw Data
Reading Template Data
Reading Complement Data
Reading Template FASTQ
Reading Complement FASTQ
Reading 2D FASTQ
Done
Object of class: Fast5Summary
Contains information from:
  5 fast5 files
  |- 5 template strands
  |- 5 complement strands
  |- 5 full 2D reads

 

ADD COMMENTlink written 3 months ago by Mike Smith1.7k
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