ShortRead Error message: invalid character '
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@laurenfitch-11575
Last seen 2.4 years ago

Hi, I am trying to read a series of FASTQ files into R with the ShortRead package. It reads the first four files fine but gives an error on the fifth:

> test <- readFastq(buddy.file.list[[5]])
Error: Input/Output
  file(s):
    /sbgenomics/project-files/_5_buddy_0001.fastq
  message: invalid character '

Is the invalid character the single quote? Or is it not specified in the error message? There are single quotes in all of my files, but this is the only one that isn't being read.

shortread fastq • 746 views
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@laurenfitch-11575
Last seen 2.4 years ago

The invalid character was a space. I was reading simulated FASTQs from PBSIM and it created some reads with spaces. Leaving this up in case it's helpful for anyone else.

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How did you fix the output fastq?

I am having similar problem with fastq generated from guppy_basecaller. Seems only recently that the generated fastq throws error with ShortRead.

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fastq is such a simple format it seems odd that a program would generate invalid files. Maybe you've moved the file between computer operating systems in a way that has corrupted them? These files are plain text files, so if there is a problem you could in principle open it in any text editor, but the file could be too large for standard tools. It seems better to figure out where the problem is introduced.

What platform are you on? What specific message does ShortRead report?

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