fastq to fastqsanger stuck in orange

usegalaxy.eu support
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1

I encountered an issue: I was working on (https://usegalaxy.eu/) and trying to convert some files from fastq to fastqsanger using the pencil tool but this triggered a “Metadata is being auto-detected” operation on each file. Each file is stuck in orange and unusable. My username is titomontenegro.

Here is everything that I know:

The dataset is stuck in orange for days.
There are no standard output/error messages
The job API ID is 11ac94870d0bb33a56262f9445dd7ea7.

Any help is appreciated.

2

Hi @biotemon

You shouldn’t need to do this conversion.

What to try instead:

  1. Let Galaxy auto-detect the datatype of files during Upload. Most fastq will be detected as “fastqsanger” now.
  2. Run FastQC on the files. If “Illumina 1.8+” or greater is detected for the quality score scaling, then the data is “fastqsanger”, meaning the quality scores are scaled as Sanger Phred+33.

I’m guessing that the original datatype assigned wasn’t correct. Maybe the data is compressed but not labeled that way (guess!)? The datatype needs to match the actual content of the file – and it is possible to override that.

So, try the help above for this as well. If Galaxy doesn’t guess the datatype correctly for fastq reads, that means something more is going on. The file could be corrupted from some upstream data transfer or manipulation step.

This tutorial covers how to interpret fastq data → NGS data logistics