MITObim usage

[marco91sol]

I launch the following command: ./MITObim.pl -end 10 -quick ~/COI_sequence.fasta -sample CS_test -ref reference-mt -readpool ~/CS/Illumina_reads/CS.fastq &>log

It gives me as output the following: Can't exec "mirabait": No such file or directory at ./MITObim.pl line 286. your readpool does not contain any reads with reasonable match (k = 31) to your reference - Maybe you ll want to try different settings or even a different reference?

How can I solve this?

[conchoecia]

You need to install mira 4.0.2 and put it in your PATH so that your system can find it. There is a pre-compiled binary in this MIRA install, so you don't have to compile the program by running make, et cetera.