Hello,
Check that you are using the latest version of these tools and update them if not:
https://toolshed.g2.bx.psu.edu/view/iuc/sra_tools/1790dcf3c32d
There was an earlier problem with extracting fastq data from SRA archives (now fixed). A newer issue with extracting bam data is undergoing a fix. So, upgrade now, then watch for the next update (should be soon).
Related issues/tickets for these tools: https://github.com/search?q=org%3Agalaxyproject+ncbi+tools&type=Issues
FAQ that explains how I found the known issues.