No polished contigs despite ~50X coverage
Opened this issue · 5 comments
I've used Racon on > 200 assemblies and have only had this error arise with one sample...
The reads in this case are ONT reads that I mapped to my assembly using Minimap2. The coverage distribution (removing the high coverage tail) looks like this...
When I run Racon, everything looks normal, there are no errors, and it ends with
[racon::Polisher::] total = 24.029181 s
The output file, however, is empty. When I run with '-u', the output file gets properly filled with all the unpolished contigs.
I'm thinking this has something to do with the input reads as I have two different assemblies I've made for the same sample and both are having the same issue. Any ideas?
Hello,
can you please paste the whole racon log?
Best regards,
Robert
Of course...
[racon::Polisher::initialize] loaded target sequences 0.072242 s
[racon::Polisher::initialize] loaded sequences 6.214936 s
[racon::Polisher::initialize] loaded overlaps 5.285117 s
[racon::Polisher::initialize] aligning overlaps [====================] 4.301526 s
[racon::Polisher::initialize] transformed data into windows 0.978941 s
[racon::Polisher::polish] generating consensus [====================] 0.563739 s
[racon::Polisher::] total = 17.828767 s
Do you have a fastQ file? If so, what is the average quality score?
This is a published read set I pulled from NCBI and appears to be missing all quality info. No idea why...
Could you provide the data for this example?