TopHat error message


I am quite unexperienced with Galaxy and I am currently doing the course “Genomic Data Science with Galaxy” in coursera. In the course we are supposed to run TopHat (I know it is not the best tool but I need to use it for this course) on a few datasets but unfortunately I got an error message for every dataset. Please see below an example of the error. Is there something wrong with TopHat in Galaxy or am I doing something wrong? I cannot advance with this course until I get this sorted so any help would be very much appreciated. Thank you!


Dataset Information

Number: 45
Name: TopHat on data 1: accepted_hits
Created: Mon Sep 14 19:52:37 2020 (UTC)
Filesize: 10.6 MB
Dbkey: hg19
Format: bam

Job Information

Galaxy Tool ID:
Galaxy Tool Version: 2.1.1
Tool Version: TopHat v2.1.1
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 0
Job Messages * Fatal error: Tool execution failed
  • Log: tool progress
  • Log: tool progress|
    |History Content API ID:|bbd44e69cb8906b526b75470c3a45f6f|
    |Job API ID:|bbd44e69cb8906b502d4b2a07cc732dd|
    |History API ID:|05bd347e25cb16ee|

Tool Parameters

Input Parameter Value
Is this single-end or paired-end data? single
RNA-Seq FASTQ file * 1: Cd20_Rep1
Use a built in reference genome or own from your history indexed
Select a reference genome hg19
TopHat settings to use preSet
Specify read group? no
Job Resource Parameters no

Inheritance Chain

TopHat on data 1: accepted_hits

Job Dependencies

Dependency Dependency Type Version
bowtie2 conda 2.2.8
tophat conda 2.1.1

Dataset peek

no peek