Error in running Spades assembly

Hi everyone! I am trying to run SPAdes on galaxy.eu , I have uploaded my paired ends ( after trimming) and specificed my work conditions. But the assembly is stopped by the following error " No assembly mode was specified. if you intend to assemble high coverage multi-cell/isolate data, use --“isolate option” .

I don´t see any assembly mode to be specified in the settings of spade and also I have tried to run it whith the “isolate” option on, but it said it was incompatible with the “careful” option that I would need for my analysis.

Does anynone have an idea on what should I change? or any other tip?

Thank you all.

Welcome, @davide_bersanetti

I think I understand your question – you want to use an option with the tool that some of the other options are incompatible with, yes?

If that is a parameter combination that is incompatible with SPADes itself, then remember that the tool is the same in Galaxy as anywhere else. The only difference is that we put a web interface on top to make constructing the command line easier. So – increased accessibility, and the underlying algorithm is still the same.

What to do

  1. Check the SPADes tool documentation – is what you want to do possible?

  2. If possible, does your query meet the requirements for that? Meaning: sometimes parameter combinations are dependent on characteristics of the input, so confirm that as well.

  3. Then try to apply that logic onto the Galaxy form.

  4. If you need help with any of this, you can share what you have now (screenshots?) and we can help to confirm what might be going on. Most tool forms have “every” option but there are some practical limits at the public servers. We can clarify and make development requests as appropriate.

Hope this helps! :slight_smile:

Hi Jennai,
thank you for your help and response

The problem is that it says " no assembly mode specified" which I really don´t know what it means since there is no way to specify it.
I solved the problem by using another workflow (shovill).

The option I wanted to use was the carefull option and by looking at tutorials and previous works, it is totally possible ( i have added trimmed paired sequences and also unpaired trimmed sequences as additional reads in the dedicated section), so I don´t know what was going wrong.