quick option error: no reads with reasonable match

[jullee]

(I see that this question has been asked by others before here and on the Google Group but I don't think it's actually been answered).

I'm using MITObim to assemble the chloroplast genome of a sample with a reference genome from the same species. I've managed to get the two-step approach working (using MIRA), but wanted to also see if the --quick option would produce similar results. When I run the quick option I get this error:

Can't exec "mirabait": No such file or directory at /Linux/MITO/MITObim.pl line 286.

your readpool does not contain any reads with reasonable match (k = 10) to your reference - Maybe you ll want to try different settings or even a different reference?

As you can see, I've already played around with different kbait settings (20 and 10). Any additional suggestions would be useful. It's strange to me that it works with the two-step process but not the quick option.

For reference, my exact command is:

/Linux/MITO/MITObim.pl -start 1 -end 30 -kbait 10 -sample ann802 -ref test_annuus_cp_genome_quick -readpool ~/sunflower_organellar_genomes/MITObim/ANN802_paired_interleaved.fastq -quick ~/sunflower_organellar_genomes/MITObim/sunflower_cp_DQ383815_noIRa.fasta >& log

log_quick.txt

And my log file is attached.

[chrishah]

Hi,

Thanks for your patience - Sorry for the delay!
The main error seems to be that the mirabait executable can't be found. Which is surprising, since you say you got the two step protocol working and I would have thought that this issue would come up there as well. perhaps you ran the 2step on a different system than you are trying the quick one now..

Anyway - can you make sure that mirabait is in your path, please? So, if you just type mirabait -v it should say '4.0.2' and do not give an error. Then it should work.
If for some reason you can't/won't put the executables into your path you can specify the location of the mira executables in the command line via the option --mirapath <absolute path to the directory that contains the mira executables>. Please try that and let me know if it works.

Best wishes,
Christoph

[jullee]

Hi I am confused why the quick option needs the mirapath? I thought that in the quick option/direct reconstruction (Tutorial II) only MITObim is used?

[chrishah]

Hi,

Even with the quick option MITObim uses two programs from the MIRA package, that is mirabait (baiting reads that have some match to your reference/bait) and then mira (the actual assembler). MITObim just wraps around the process and repeats it until done.
Best wishes,
Christoph

[jullee]

Ok perfect. Thanks for the explanation.

…

On Mon, Dec 3, 2018 at 12:31 PM Christoph Hahn ***@***.***> wrote: Hi, Even with the quick option MITObim uses two programs from the MIRA package, that is mirabait (baiting reads that have some match to your reference/bait) and then mira (the actual assembler). MITObim just wraps around the process and repeats it until done. Best wishes, Christoph — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#36 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALXEQyVEUAeCh3gpklAGKW7lWE5mWjb4ks5u1Yo5gaJpZM4YQ0Zf> .

[iseiblitz]

Hi!

I have a similar issue as jullee but after giving mitobim the full path on mirapath, the "can't exec mirabait" message disappeared but the "no reasonable match" message remains (my log file is attached as log02.txt). I wonder if it can be related to the fact that I am using mitobim on Ubuntu 16.04 LTS for Windows 10 instead of on an actual Linux machine. Is there a solution for that?

An off topic comment is that I have tried mitobim on Docker and it works but it seems to be using only one thread in my computer (my processor is an i7 8th generation), so I thought I could speed things up by running mitobim directly on Ubuntu for Windows.

Thank you in advance for your support and, moreover, thank you for creating mitobim! Despite a few bugs, it has helped me a lot!
Isabela

log02.txt

[tanglp11]

Hi!

I have a similar issue as jullee but after giving mitobim the full path on mirapath, the "can't exec mirabait" message disappeared but the "no reasonable match" message remains (my log file is attached as log02.txt). I wonder if it can be related to the fact that I am using mitobim on Ubuntu 16.04 LTS for Windows 10 instead of on an actual Linux machine. Is there a solution for that?

An off topic comment is that I have tried mitobim on Docker and it works but it seems to be using only one thread in my computer (my processor is an i7 8th generation), so I thought I could speed things up by running mitobim directly on Ubuntu for Windows.

Thank you in advance for your support and, moreover, thank you for creating mitobim! Despite a few bugs, it has helped me a lot!
Isabela

log02.txt

Hi! Have you resolved this? I have the same issue, but I'm using it directly in Linux.

[iseiblitz]

Hi!
I have a similar issue as jullee but after giving mitobim the full path on mirapath, the "can't exec mirabait" message disappeared but the "no reasonable match" message remains (my log file is attached as log02.txt). I wonder if it can be related to the fact that I am using mitobim on Ubuntu 16.04 LTS for Windows 10 instead of on an actual Linux machine. Is there a solution for that?
An off topic comment is that I have tried mitobim on Docker and it works but it seems to be using only one thread in my computer (my processor is an i7 8th generation), so I thought I could speed things up by running mitobim directly on Ubuntu for Windows.
Thank you in advance for your support and, moreover, thank you for creating mitobim! Despite a few bugs, it has helped me a lot!
Isabela
log02.txt

Hi! Have you resolved this? I have the same issue, but I'm using it directly in Linux.

Hi! To be honest I haven't gone back to it because I ended up being able to use it on a Mac and on a Linux machine. So I am afraid I can't help much. But it works on actual Linux... Hope you can get it sorted!