Forum:possible bug: can make minia run forever with a bogus FASTA
1
0
Entering edit mode
9.2 years ago
adam.ewing • 0

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

``1

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 • 2.0k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
4
Entering edit mode
9.2 years ago
Rayan Chikhi ★ 1.5k

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 COMMENT

Login before adding your answer.

Traffic: 1084 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6