Thanks a lot for your answer. I used FASTQ groomer to convert fastq format to fastqsanger. I started the mapping of my reads to the reference, without problems, however Galaxy does not reach the loading process. This gives me the message:
"A job has been successfully added to the queue - resulting in the following dataset:
58: Map with BWA for Illumina on data 51, data 49, and data 5: mapped reads
You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered."
But Galaxy does not end the task (even after waiting for more than an hour). Why is that? I have several mappings to perform and is a bit frustrated about that I cannot accomplish even one. Hope anyone can help me with that issue.
Tool name: Map with BWA for Illumina
Tool version: 1.2.3
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3
ToolShed URL: http://toolshed.g2.bx.psu.edu/view/devteam/bwa_wrappers