Question: Errors with larger kmers
0
gravatar for hiimwalker
2.8 years ago by
hiimwalker0
hiimwalker0 wrote:

Hello,

I like the concept of using your dsk program to assist with my assembly. I have a file with assembled reads with very deep coverage (600k) of a very short sequence (215-270bp), and analyzing the sequences with this program is a wonderful treat. However, I had trouble at first installing the current version properly to allow for selection of 215-mers, even after attempting to recompile with

rm -Rf CMake* && cmake -Dk4=250 .. && make

The newest version of the program seems to get upset if I try a kmer bigger than 127. I looked around these posts and found someone who had a similar problem, where you suggested to download http://gatb-tools.gforge.inria.fr/versions/src/dsk-2.0.3-Source.tar.gz, which seemed to work wonderfully at first, but now I'm getting an error saying I should contact a developer, so here I am. Any help would be greatly appreciated!

dsk -nb-cores 16 -file 7.fastq -kmer-size 215 -out dsk_output.txt
[DSK: Collecting stats on read sample   ]  100  %   elapsed:   0 min 3  sec    estimated remaining:   0 min 0  sec   cpu: 1565.3 %   mem: [ 72,  72,  72] MB
[DSK: Pass 1/1, Step 2: counting kmers  ]  51.5 %   elapsed:   0 min 10 sec    estimated remaining:   0 min 9  sec   cpu:  831.7 %   mem: [821, 852, 852] MB
EXCEPTION: OAHash: max rehashes reached: 26214400 (notify a developer)
kmer amplicon • 866 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by hiimwalker0

Tagging: Rayan Chikhi

ADD REPLYlink written 2.8 years ago by genomax65k
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