isovic
layer begin and end positions are invalid!
I am getting an error
[racon::Window::add_layer] error: layer begin and end positions are invalid!
I ran racon twice and I get the same error. Any help or suggestion?
Hello, which racon version are you using? Could you provide the data that is causing the error?
Best regards, Robert
I am using version 1.2.0. The data that I am using is very huge (5.1GB compressed). I aligned the reads using minimap. The output SAM output is then the input for racon. I am doing minimap-racon twice. In the first round, racon completed successfully. I get this error in the second round.
Could you please try the second iteration with the latest racon version (1.3.3)?
Here some more lines just before the error.
[racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 668099/668099 [racon::Window::add_layer] error: layer begin and end positions are invalid!
sure. I will try with the latest racon version and let you know. Thanks
I think the latest release is 1.3.2. I could not find v1.3.3 in github releases.
Versions 1.3.3 (latest commit on master, but not a release) and 1.3.2 are almost the same, the newer one has a smaller log while runnig.
Best regards, Robert
We just found out that our genome assembly has a duplicated contig name. Can this duplicated naming error cause this error?
Nope. Have not got chance to run. I just found out at there is a duplicated contig name this morning. I got new assembly without duplicated contigname. I will try with this new assembly now. Our HPC has v1.3.2 installed. I am thinking to test with v1.3.2 for now as , according to you, there is not much difference between v1.3.2 and v1.3.3, except the log filesize.
Racon ran successfully now. I ran racon-1.3.2 and with the no contig name duplication. Thanks for the help.