Error encountered in mt_assembly using mitoz all command

[timz0605]

Error encountered in mt_assembly using mitoz all command

[timz0605]

I think I might have found out how the error was encountered... For the option Clade and requiring_taxa, the option Porifera-sponges always give me an error during the mt_assembly step (since I am working with sponges and cnidarians). However, when I use Arthropoda as the clade, everything now works fine. I am wondering if this is a bug that needs to be fixed since I have tried updating the ete toolkit.

[linzhi2013]

Hi Timz0605,

Thanks for reporting the issue.

I will check the program later, I don't know if there are bugs.

And yes, you can also try Arthropoda or Chordata for the -clade option (but you should also set the correct genetic code for your sample)

You can have a look the DM01.megahit.hmmtblout.besthit.sim.filtered-by-taxa.high_abundance_10.0X and DM01.megahit.hmmtblout.besthit.sim.filtered-by-taxa.low_abundance.fasta to learn if the below message is true or not:

mitoz.utility.utility - WARNING - filter_by_abundance(): All sequences are low abundance (<10X)

(See https://github.com/linzhi2013/MitoZ/wiki/Tutorial#2-the-mitogenome-assembly-step)