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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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layer begin and end positions are invalid! #118

Open TSL-RamKrishna opened 5 years ago

TSL-RamKrishna commented 5 years ago

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?

rvaser commented 5 years ago

Hello, which racon version are you using? Could you provide the data that is causing the error?

Best regards, Robert

TSL-RamKrishna commented 5 years ago

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.

rvaser commented 5 years ago

Could you please try the second iteration with the latest racon version (1.3.3)?

TSL-RamKrishna commented 5 years ago

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!

TSL-RamKrishna commented 5 years ago

sure. I will try with the latest racon version and let you know. Thanks

TSL-RamKrishna commented 5 years ago

I think the latest release is 1.3.2. I could not find v1.3.3 in github releases.

rvaser commented 5 years ago

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

TSL-RamKrishna commented 5 years ago

We just found out that our genome assembly has a duplicated contig name. Can this duplicated naming error cause this error?

rvaser commented 5 years ago

Probably! Did you manage to run the newer version? Any errors there?

TSL-RamKrishna commented 5 years ago

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.

rvaser commented 5 years ago

Sure, go ahead.

TSL-RamKrishna commented 5 years ago

Racon ran successfully now. I ran racon-1.3.2 and with the no contig name duplication. Thanks for the help.