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)
Tagging: Rayan Chikhi