I am a galaxy user at Hunter College in New York. Recently we have encountered mismatching files throughout various tools under the same history. We are running our RNAseq analysis on the Dockerized containers. I need the BAM files (accepted hits) which produced by Tophats for the MulticovBed to get the read count. Those BAM files should be the binary 'accepted hit' files but instead they are showing random output from other tools(see the image below). This not only happened to BAM files but for most of the tools and most of the datasets. For example, the output for Groomer is not actually from Groomer but rather from the Tophat 'deletion' or an output from Cufflinks. 

We are not sure if you are familiar with this issue whether it's a container or a Galaxy known issue. It would be great if you could point me to a right direction on how to resolve this issue.

Sincerely,

Changsu