I double checked your job. The same dataset (number 24) was input for both the forward and reverse reads of the pair.
In this tutorial, the reads with a
_1 are forward and with a
_2 are reverse. There are four fastq datasets that combine to make two pairs. Run the QA/trimming steps on all four, then run Tophat in paired-end mode using one of the pairs (two fastq inputs). Then run Tophat on the other pair (the remaining two fastq inputs). Later on, you can learn how to do batch job submission in the tutorials linked below.
The tutorial you are using is older and still functions correctly as far as I know. Just be aware that Tophat/Tophat2 is considered deprecated now and replaced by HISAT2, so after learning and ready to do your own analysis, you'll want to use the latest tools and workflows.
Galaxy tutorials (the most current): https://galaxyproject.org/learn/
Support FAQs: https://galaxyproject.org/support/#troubleshooting. Start here next time you have a job fail: My job ended with an error. What can I do?
Thanks, Jen, Galaxy team