I’m going, a little slowly, through the Guide—questions of time.
I have a problem and I will try to describe it.
I arrived at the RMSD analysis, seemingly, without problems.
When I ran the RMSD analysis I had the error (red).
The first thing that I controlled was the files necessary to complete the RMSD. In the files, I found the file nr.40 “GROMACS Production simulation checkpoint (CPT)” shows a strange view with strange characters. I repeated the “GROMACS simulation (Galaxy version 2020.4+galaxy1)” another two times having the same strange characters in the file CPT.
I decided to see the precedent files and arrived at the first file with strange characters, nr. 33 “GROMACS simulation NVT Checkpoint (CPT)”. At least I believe this is the beginning of problems. I repeated the running of the app having the same problem.
I’ve run through the tutorial, and it seems to be working Ok. This is my shared history with the output from both workflows linked into the tutorial if you want to use it as a reference “answer key” history. Compare your tool settings at each step to learn where things went wrong. I’ll leave it shared for you or for anyone else that may run across this post later.
Next time, if a tutorial has a workflow, running that yourself is a way to create this kind of answer key yourself.
Then, for your observations about the odd characters – that is expected since the data is in a compressed (binary) state. You can still attempt to view compressed data but the output will have all of the odd characters since it isn’t a plain text datatype. The job logs and parameter choices would be a better place to review what happened. You can find all of the parameters that were set for any job in a summary using the i-con.
