racon: layer begin and end positions are invalid
Hello, I have got exactly sample error as issue #118 , that is
[racon::Window::add_layer] error: layer begin and end positions are invalid!`
I am using racon 1.3.3 and here is my command:
racon -t 20 all_pass_reads_without_lambda.fasta minimap2_to_flye_sorted.sam assembly.fasta > assembly_racon_r1.fasta
I have checked and there are no duplicate contig names in the assembly like #118. Please can someone advise on how can I fix this error?
Many thanks, Urmi
About this issue
- Original URL
- State: open
- Created 5 years ago
- Comments: 26
Haha, happens 😃
Best regards Robert
Well. How to say… super embarrassing mistake on my side.
The alignment file was the problem. Instead of mapping reads to the assembly I mapped them against themselves. So stupid copy/paste error.
Now it finished without errors and super fast!
Thanks for your help Robert!
cheers Michael
Running the full dataset with PAF files worked like a charm. Thank you so much once again, Robert. 😃