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?
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
Check the SPAdes tool documentation – is what you want to do possible?
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.
Then try to apply that logic onto the Galaxy form.
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.
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.
Thanks for explaining a bit more, and great that you have Shovill working!
If I am understanding your current parameters correctly, the tool is expecting you to combine the Operation Mode and the Pipeline options parameters in a logical way the underlying tool can support.
Please feel free to add more details over there at Github or here as extra comments. Screenshots would help – everything on the job details (using the i-icon) view. We’ll need to see the input/parameter table + full error messages fully expanded. I’m curious what the other parameters you set were, and the type of read data might matter too. This would help the developers to learn exactly how your error was produced so we can make sure to include your use-case in any changes we make.
Hopefully this helps! You should be able to use the SPAdes guide to understand the parameter combinations, and other assembly tools might offer more choices as you have discovered already.
As a sort of quick guide to help you right now, and maybe others reading later, I created a demonstration history. Anyone can click to review and even import to get a closer look or to try out parameters with smaller yet representative data.
I added tags to the history with the different assembler modes combined. This means you can do things like click on a tag to find all the other runs that share a parameter (like “careful”) or with the same result (“successful” or “failed”).
note: dataset 19 in this history is probably using the same parameters as used in the original reported error in this topic.
Pipeline options – one or more of these optional modifiers. Note that some choices will require a specific choice with the Operation mode above (usually the default choice Assembly and error correction).
