mtDNA genome assembly using MITObim not working!

[JackieBadger]

Hi,

Has anyone used MITObim with success?

MITObim either quits on iteration 0 without giving a detailed error message or the log file says that it has started but nothing happens.

I am trying to build a mtDNA genome from a COI bait sequence, using MiSeq fastq's and the following parameters:

./MITObim.pl -end 100 --quick ./COI.fasta -strain fish1 -ref fish1COI -readpool ./fish1_interleaved.fastq --noshow &> log

any help would be much appreciated.

Thanks,

J

[rmdoyle]

I was going to play with MITObim this evening, I'll let you know if I have any success.

[JackieBadger]

Think I had the wrong version of Mira installed

[rmdoyle]

So you were able to get the MITObim.pl script to work with MIRA 3.4, but not other versions of MIRA? We have MIRA 3.9 installed on our cluster currently, so it would be nice to not have to install an older version.

[JackieBadger]

I had Mira 3.4 not Mira 3.4.1.1

Mira 3.9 is a different beast all together