Segmentation fault when using Minia 3 about minia

[rchikhi]

Looks like it's the same bug as GATB/bcalm#31
It's being investigated right now. Are you able to reproduce it on a smaller test set by any chance?
Best,
Rayan

[zifanzhu]

Hi Rayan,

Thanks a lot for your quick response!

I actually have four datasets (all of size greater than 1T) to assemble. Minia 3 succeeded in the other three. Do you think it's a good idea to run Minia 3 on this failed dataset again but only using a small part of it?

Best,
Zifan

[rchikhi]

Hmm it's hard for me to give a definitive answer to that. Maybe, and/or also change the k-mer size. It sounds like 19 is very low for a 1TB dataset.

[zifanzhu]

Hi Rayan,

I used KmerGenie to estimate the best k. Here is the final output from it:

It also mentioned the coverage cut-off for the best k should be 33. I'm not sure if this corresponds to the "-abundance-min" option in minia. I just used the defaut value (2). Probably I should change to 33 if that's the problem?

Btw, I can definitely try larger k. Thanks for your advice!

Best,
Zifan

[rchikhi]

Hi Zifan,
Well, if kmergenie said it, then alright :)
The recommended coverage cut-off indeed corresponds to -abundance-min but 33 seems absurdly high, especially for such a low k value. Could you please share the histograms to me? [email protected]
BTW I've committed a tentative fix for your segfault, are you able to recompile Minia yourself?
The steps are:

cd minia
cd thirdparty/gatb-core/gatb-core
git pull
cd ../../../
cd build
make -j 8

Rayan

[zifanzhu]

Thanks Rayan! I've sent the histograms via email with subject 'K-mer histogram for issue #15'. Yes I can compile Minia myself and will try this fix!

Best,
Zifan

[zifanzhu]

Hi Rayan,

I reran Minia with the tentative fix and it worked smoothly. Thanks for your help!

Best,
Zifan