Forum: possible bug: can make minia run forever with a bogus FASTA
0
gravatar for adam.ewing
24 months ago by
adam.ewing0
Australia
adam.ewing0 wrote:

I tested minia (2.0.2, 64 bit, precompiled binary) on a FASTA file with one entry consisting of a single base i.e.:

>test
A

Which leads to it running forever while outputting status messages. Obviously this isn't a significant issue as nobody in their right mind would feed such a file to minia, but in an automated setting this can happen if something goes wrong upstream. Anyway, thanks for a great assembler!

-Adam

minia forum • 726 views
ADD COMMENTlink modified 24 months ago by Rayan Chikhi1.1k • written 24 months ago by adam.ewing0

It's great that you posted this here. Other users of minia might find it useful if their execution of it hangs. I changed the post type to "forum" since you're not really asking a question.

However, if you want a high chance of getting the developer's attention, you will probably have better results if you report this as a bug on the github repository.

ADD REPLYlink modified 24 months ago • written 24 months ago by Dan D5.9k

No, here is perfect. I get notifications for any post with the "minia" tag. That github repo, however, isn't for Minia itself, but for a docker image that wraps it. The actual git repo of Minia is hosted by our institution (Inria), not Github, for now.

ADD REPLYlink modified 24 months ago • written 24 months ago by Rayan Chikhi1.1k
4
gravatar for Rayan Chikhi
24 months ago by
Rayan Chikhi1.1k
France, Lille, CNRS
Rayan Chikhi1.1k wrote:

Thanks for the feedback!

We've recently noticed a possibly related bug with tiny k values, due to optimizations in the k-mer counter. Values of k<=4 will be forbidden in Minia version above 2.0.3, which should address this issue as well.

ADD COMMENTlink modified 24 months ago • written 24 months ago by Rayan Chikhi1.1k
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