Hello,
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!
TopHat
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: | toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1 |
|---|---|
| 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|
|UUID:|196af60a-45aa-4a72-81a0-d2ad55bd4cc1|
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