Problem with annotation

[kabilov]

on which platform/server? (Windows? Windows Sublinux? MacOS? Ubuntu? etc.)

Ubuntu 18.04.6 LTS

MitoZ version?

3.6

How did you install MitoZ? (e.g. Docker, Udocker, Singularity, Conda-Pack, Conda, or source code)

Docker

Did you run a test after your installation, and was the test run okay?

Test was Ok

How much data (roughly) did you use for mitogenome assembly? e.g. 5Gbp?

It was used Annotation only

The command you used?

mitoz annotate --fastafile NC_012920.fa --genetic_code 2 --clade Chordata --thread_number 32 --outprefix test

Problem description

I downloaded the reference human mitogenome NC_012920 and annotated it using MitoZ. The annotation results raise questions. The ND2 gene contains a large number of stop codons. Most related specie is Homo heidelbergensis.
When the --clade Chordata command is omitted, the closest species becomes Aleurodicus dispersus, and ND2 does not contain stop codons.

Log messages from MitoZ (stdout and stderr, e.g., both m.log and m.err files)

NC_012920.log

[linzhi2013]

Hi @kabilov ,

Thanks for reporting the issue!

I tested your command

mitoz annotate --fastafile NC_012920.fa --genetic_code 2 --clade Chordata --thread_number 4 --outprefix test

and the problem can be repeated. (but I didn't test "When the --clade Chordata command is omitted", since its default value is Arthropoda)

There could be some bugs in MitoZ, I will have a look at it in detail when I have time.