mitogenome lost

[JWDebler]

Hi,
I just ran raven over some of my nanopore data, and the assembly looks great, with one caveat, it lost the complete mitogenome. The same reads assembled by Canu lead to more fragmented contigs, but a tandem repeat of 3-4 mitogenomes. NECAT assembled the mitogenome into a single copy contig, but Raven seems to have discarded all the mitogenome reads as I cannot find any of the mito sequences anywhere in the assembly.
Any idea what happend or how to find out?
Cheers.
Raven.Cereal file

[rvaser]

Hi,
I'll check the cereal file, but please tell me the Raven version you are using.

Best regards,
Robert

[JWDebler]

@rvaser Sorry, was away over the extended easter break. That was with version 1.5.0

[rvaser]

What is the expected size of the mitochondrial DNA? I inspected the cereal file but not sure what to look for.

[JWDebler]

It's 52504 bp. Would the sequence help?

[rvaser]

It could help :)

[JWDebler]

Here you go: mitogenome.zip

[rvaser]

@JWDebler, I inspected the GFA in more detail, there is a contig consisting of two reads that has 2.5x the mitochondrial genome. Raven did not print it as it is not circular and has only two connected reads. Sorry for the huge delay.