Greetings everyone. I am currently working on clinical klebsiella pneumoniae DNA samples on Galaxy and I am trying to run Staramr tool to find AMR genes.
Whenever i enabled the PointFinder database search and selecting Klebsiella (unvalidated), the tool always fail to run.
Disabling the PointFinder makes the Staramr tool able to run and give results.
Is there anyway to overcome this problem or is there another alternative tool which can be used to find the mutations in my samples?
Many thanks.
Welcome, @Ahsan_Jafar
You didn’t state which server you are working at … but I’ve started up a test at the UseGalaxy.eu server. This is using tool test data, so a very small dataset, but might flush out what is going on.
https://usegalaxy.eu/u/jenj/h/test-staramr
These unvalidated indexes might produce more details or reports inside of the job logs for a tool failure. If yours have any messages, you are welcome to post more details about those. Please see the banner at this forum for how to, or here How to get faster help with your question
I’m asking for that because and I wasn’t sure if the tool is failing, or reporting some kind of “can’t process this data” result, meaning: are you getting a technical tool failure or a scientific failure? The latter is what I’m hoping the test will reveal, but your data could produce something different, and we can try to help to interpret it here.
For alternative tools, try a search with the keyword amr at the UseGalaxy.eu server – I see four others as of this afternoon.
Let’s start there, thanks! 