FastQC-SequenceFormatException: Midline '@9###' didn't start with '+' at 27122723

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1

What should I do？
Failed to process file ERR1600427_2_fastq_gz.gz
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline ‘@9###’ didn’t start with ‘+’ at 27122723
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:179)
at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:129)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
at java.base/java.lang.Thread.run(Thread.java:1623)

2

Hi @Sanji

This means that your fastq file has a format problem.

Some reasons that can happen

  1. Wrong datatype assigned to a dataset. You can try to redetect the datatype → FAQ: Detecting the datatype (file format)
  2. The file was truncated at some step. You could try to Upload again → Getting Data into Galaxy.
  3. If that is not enough, you’ll need to check the file before it was loaded to Galaxy.

When loading data, try using all default settings. If Galaxy guesses the wrong datatype, that can be a warning that something in the file isn’t what you expected it to be.

This tutorial explains more about fastq format itself → Hands-on: NGS data logistics / Introduction to Galaxy Analyses

Please give those a review, and if you need more help, please share your history and we can take a quick look. If you are following a tutorial, please also include a link to that tutorial.

Let’s start there, thanks! :slight_smile: