Hi,
This is my first time to use Pavian, how long does it take to complete the run for Kraken files in Galaxy? Mine has been running for more than a day, I am not sure if the files need to be converted into any other version? Please help!!
Thank you.
Welcome @Priya_Samson
This is an interactive tool, so things should start up quickly, maybe 10 minutes maximum from what I know, and a day is much too long.
Are you following this tutorial? If not, it can be a helpful guide for getting the input data formatted in a way the tool can understand. → Hands-on: Taxonomic Profiling and Visualization of Metagenomic Data / Taxonomic Profiling and Visualization of Metagenomic Data / Microbiome (#visualization-using-pavian)
Other than that, I am curious about which server you are working at. Maybe more is going on with getting the environment launched. You are welcome to share you history but if you just want to note the URL of the server, I can run an independent test to confirm all is working as expected now.
And, if this was at UseGalaxy.org, you might be able to simply restart it. We had a small cluster issue earlier today, plus the server restarted for a minor software adjustment. Either could cause an interactive tool to stall out for a short window, and some tiny fraction of jobs may have been impacted.
Let’s start there! 
Hi,
Thank you for the response, I am working using UseGalaxy.eu. In fact, I tried to interrupt the run and restarting again, thinking if my internet connectivity was slow, but the issue is still persisting. Like now it’s about 3 hrs again, it’s showing job info running.
Ok, thanks for checking! I was able to start up my test and I ran it twice. Each time it launched correctly. I used a Kraken2 report input. Is this what you were using? The file itself might be a different type, and the tool is having trouble reading it in and that is stalling the environment for some reason.
Would you like to share back your history with the starting file(s)? Please leave the failed tool launches in their current state so I can mirror your settings (you could also screenshot whatever else you think is informative!). I’ll be able to get a copy and test the launch the same way you are doing this, plus give feedback about the file contents.
How to generate the share link is in the banner of this forum, also here → FAQ: Sharing your History. You can paste the link back here in your reply.
Small note: it is important to only run one interactive tool at a time, or the subsequent runs will not start. It already looks like you only have one in your list so I’m just mentioning this for whoever else may find this topic later who has a similar issue.
Hi, the first file i uploaded was the Kraken2 report, since it took longer like more than a day. THe second run i tried uploading the converted Kraken2 Just to see is it makes any difference, but it looks all the same. Back history link is here: Galaxy.
And yes, I have been using only Pavian and not any other tool.