No output produced

[shamir-lab]

No output produced

[dpellow]

Thanks for your interest in using Recycler.
Does the Recycler run complete without producing output or is it getting stuck during the run? If there are many short contigs besides the 7 long ones you mentioned, Recycler could just be taking a long time to complete running.
Recycler will only assemble plasmids from overlapping contigs that form a circular path and have mostly uniform coverage. If this is not the case in your data then Recycler will not assemble plasmids.
Otherwise, we can help you to debug if you can send us more details of the dataset.
Hope that helps!

[sum732]

Thank you for the quick response.
Recycler does complete the run and finishes with no output. From "SPAdes" there are short contigs as well.
Here is what is shown on STDERR:

(7.5625, 430.5257300917254, 1336.0)                                                             
================== path, coverage levels when added ====================                        
(4936, ' nodes remain in component\n')                                                          
==================final_paths identities after updates: ================  

And then empty output is produced.
For this plasmid in total there are about 70K PE reads. About the uniform coverage, that needs to be checked. Can you recommend parameters that I should try? I have changed the kmer etc with no affects. Can you recommend any other tools that you think may be useful if coverage is the issue?

[dpellow]

I can try to help you with this - send me an email at [email protected] and I'll see what I can do.