Entering edit mode
7.9 years ago
Kate
•
0
Hello,
I am trying to run abyss with larger kmer size, either >64 or >96. The abyss was initially compiled by default so I just re-configured by "./configure --enable-maxk=96 && make" as instructed. However, when I try to run -k95 there is error message coming out as below --
ABYSS: ../Common/Kmer.h:49: static void Kmer::setLength(unsigned int): Assertion `length <= 64' failed. Aborted (core dumped)
It seemed that re-compiling did not work. Anyone can provide any advice?
Meantime, I would like to run with kmer size larger than 96, anyone can help with this as well?
Thank you in advance!
Are you sure you are running the abyss program you just compiled? Did you do make install?
That's right, I forgot to do the make install. I just redo and it seems running with k95. Thank you very much!
Do you have any suggestion on running with larger kmer than k96? There is a recent paper used 127k and 247k...
Have you tried ./configure --enable-maxk=128?
Interesting and it seems okay with compiling, and now running with 125k. Thanks!
There were some other threads mentioned that the base codes needed to modified to reach more than 96 mers, however this way seems more straight forward than those.