Closely_related_species identification error #232
Description
MitoZ version?
3.4
How did you install MitoZ? (e.g. Docker, Udocker, Singularity, Conda-Pack, Conda, or source code)
Conda
Did you run a test after your installation, and was the test run okay?
Yes, and the first two lines of summary.txt are:
#Seq_id Length(bp) Circularity Closely_related_species
k99_0 16453 yes Oryzias latipes
How much data (roughly) did you use for mitogenome assembly? e.g. 5Gbp?
3
The command you used?
mitoz all
--outprefix JZ2533
--thread_number 20
--clade Chordata
--genetic_code 2
--species_name "Homo sapiens"
--fq1 JZ2533_R1.fq.gz
--fq2 JZ2533_R2.fq.gz
--fastq_read_length 150
--data_size_for_mt_assembly 3,0
--assembler megahit
--kmers_megahit 71 99
--memory 50
--requiring_taxa Chordata
Problem description
The Closely_related_species information in the summary.txt is wrong. I have a specimen that I know it belongs to the genus Alcippe, but this kind of species have similar looks so I want to make further identification using the mt genome. The mitoz worked well. And the output mt.fa has the highest Percent Identity rate with Alcippe davidi, and the second is Alcippe hueti, when it is mapped to known sequences in NCBI. This result is reasonable. However, the Closely_related_species showed in the summary.txt is Zosterops lateralis, which is a species belongs to different continents and absolutely wrong. Please see the two attached files and check the results. Does it has something to do with the Etetoolkit database? I am aware this might be a negligible problem if I can get the mt genome, but I would be very grateful if you could answer this question.
Thanks!