For anyone reading this later on:
Check your job details page using the i-icon. Do you see this within the message? Or a similar message about the fastq format? If yes, then your fastq data is not intact for some reason.
Sequence and quality length don’t match
Common reasons:
- Manipulations done somewhere else impacted the file content
- Or, a truncated file was created when moving the data between storage locations, including a potentially interrupted Upload job to Galaxy
Galaxy resources!
-
To learn about NGS reads and how to inspect them, please start here: Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses
-
To learn how to Upload data to Galaxy, please see: Getting Data into Galaxy.
-
To double check for intact files and the current state of compression, try the tool Fastq info at any UseGalaxy server.
-
To check the quality content of fastq data, try the tool FastQC.
-
To see what a simple Quality Control workflow looks like, please see → What do these FastQC results mean? - #4 by jennaj
-
More workflows can be found at:
- Training → GTN Pan-Galactic Workflow Search
- Production/HTP → https://iwc.galaxyproject.org/
- The Workflows → Public workflows tab at any UseGalaxy server
New to workflows? Start here: Hands-on: Galaxy Basics for everyone / Galaxy Basics for everyone / Introduction to Galaxy Analyses