IONiseR error when using the readFast5Summary function on nanopore data
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mv340788 • 0
@mv340788-11693
Last seen 5.3 years ago

I keep getting this error when trying to read my nanopore data

Checking file validity
Reading Channel Data
Reading Raw Data
Reading Template Data
Reading Complement Data
Reading Template FASTQ
Error in strsplit(strings, "\n") : non-character argument

This is the code I am using

library(IONiseR)
library(ggplot2)
library(gridExtra)
fast5files <- list.files(path = "C:/Users/Mike V/Downloads/upload/upload", pattern = ".fast5$", full.names = TRUE)
example.summary <- readFast5Summary( fast5files )

I have updated RStudio and made sure to update the package.  Any help would be greatly appreciated.

ioniser software error bioconductor • 928 views
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Hi.  Can you edit your post to include the output of the function sessionInfo() I'd like to check which version of IONiseR you're using as this should have been patched a while back.

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Mike Smith ★ 5.3k
@mike-smith
Last seen 18 hours ago
EMBL Heidelberg / de.NBI

Thanks for the session information.  Looking at the logs, this was patched in the developmental branch a few weeks ago.  This has now propagated to the new release of Bioconductor.  If you get IONiseR version 1.4.0 this should now work.

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mv340788 • 0
@mv340788-11693
Last seen 5.3 years ago

Here's the session info.

R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] gridExtra_2.2.1 ggplot2_2.1.0   IONiseR_1.2.3  
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mv340788 • 0
@mv340788-11693
Last seen 5.3 years ago
I updated Bioconductor and the IONiseR package but I'm still getting the same error for both of my sets of data.


Checking file validity
Reading Channel Data
Reading Raw Data
Reading Template Data
Reading Complement Data
Reading Template FASTQ
Error in strsplit(strings, "\n") : non-character argument
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] gridExtra_2.2.1 ggplot2_2.1.0   IONiseR_1.4.0
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Sorry that you're still experiencing problems.  Previously this same error was reported when ONT made some changes to the fast5 file structure that IONiseR wasn't aware of ( e.g. https://support.bioconductor.org/p/75199/)  

Would it be possible for you to make a small number of files available to me?  Perhaps the format has changed again.

Many thanks,

Mike

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I sent an email with some of the fast5 files.

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Thank you for the files.  They don't appear to be in the same format as the fast5 files I've seen before.  Have they been base called with MinKNOW?  There appears to be only the most raw signal data in there, no sign of nucleotide bases.  Perhaps they need some more processing with Oxford Nanopore's software?  Even considering that, it still has a different structure from the raw files I've seen before.

I've updated the devel version of IONiseR to catch this and print a more informative error message, and I shall see if ONT have mentioned a new format somewhere.

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I sent a few more files from a different file I was sent just to see if they are any different.  I did not actually run the device so I'll try to get more details on how the data was acquired.

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The person that sent me the data thinks there must have been an error with the base calling.  Thank you for the help though Mr. Smith.
 

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