I have followed all the steps, except in the USCS hg38 dataset, I was required to select GENCODE V47 (instead of V41 like in the tutorial and V43 in the youtube tutorial), as they selected the default in the video, so I just went with the default. I can’t imagine that would make a difference!
Guidance would be greatly appreciated! Thank you in advance!
Kate
First, try one rerun. This specific error can come up when the server is restarting, or even just by chance from a connection problem. Rare, but possible!
If that is not enough, would you like to share back your history for feedback? We can help to double check that the inputs/options were set up correctly but also report/fix any technical problems as needed.
It is great that you are learning how to retrieve data! This may seem tedious but it is a really important skill to learn a bit about how to discriminate between reference data sets, since everything else in your experiment will depend on it.
This particular data is a bit complicated. There are two different types of GENCODE track data. You will want the one without the “All” in the name. The release version doesn’t matter for this tutorial, but the underlying content of the file format, and the specific data included, does.
I think you probably picked the correct file, and something else is going on, but we can double check. Please let us know if you solve this yourself instead!
I tried rerunning the job, but continued to get error messages. I also used the most recent version of the hg38 (GENCODE V47) that you had highlighted in green as a dataset that should work.
So, here’s a link to my history: Galaxy
I hope that you are able to access it, and please let me know if you encounter any problems. I’m hopeful we can get to the bottom of this problem!
The history share link is correct but this instance of Galaxy is not public, so I cannot see what is going on exactly that way.
However, from what you are describing the data seems to be correct, and I agree that the problem is with the tool itself. It is probably with the configuration. This was a Python 2 tool and it requires a special environment. This should be reported to the administrators of the server. Everyone is likely having the same problem and they might know about it already but maybe not. At least they could give you an update!
If the bug report is enabled, then submitting that way will reach them. You can include a link to our topic here in the comments area.
The other option is to contact them using the information they provided in your account registration email. You could also scan the server homepage for a contact. The last option is to contact your instructor.
Hope this helps and let us know how this works out!
Please let us know if you solve this yourself instead!