[Abyss de novo assembly] setting 127 k-mer length

[syintel87]

"How to set kmer length as 127?"

Hello, I have a problem with setting kmer length as 127.

1. The codes below gave errors.

scha@node0:~/2_GRAPE/abyss2$ ./configure --prefix=/home/scha/2_GRAPE/abyss2/ --enable-maxk=128
scha@node0:~/2_GRAPE/abyss2$ make AM_CXXFLAGS=-Wall
scha@node0:~/2_GRAPE/abyss2$ make install

2. So I made a change with the codes.

scha@node0:~/2_GRAPE/abyss2$ ./configure --prefix=/home/scha/2_GRAPE/abyss2/127mer --enable-maxk=128
scha@node0:~/2_GRAPE/abyss2$ make AM_CXXFLAGS=-Wall
scha@node0:~/2_GRAPE/abyss2$ make install

3. As a result, a new folder '127mer' was generated which also contained two folders 'bin' and 'share'.
The program files in '/abyss2/bin' seemed to be the same as those in '/abyss2/127mer/bin'.

4. I ran programs these two 'bin' folders.

/abyss2/bin$ srun -p bigmem -c 16 abyss-pe k=127 n=10 in='chwd_R1.fastq chwd_R2.fastq' name=chwd3
/abyss2/127mer/bin$ srun -p bigmem -c 16 abyss-pe k=127 n=10 in='chwd_R1.fastq chwd_R2.fastq' name=chwd3

5. However, both of these gave the same errors.

ABYSS: ../Common/Kmer.h:48: static void Kmer::setLength(unsigned int): Assertion `length <= 64' failed.
make: *** [chwd3-1.fa] Aborted
srun: error: node92: task 0: Exited with exit code 2

6. When I checked a file, 'abyss2/config.h', it seems that MAS_KMER was set to be appropriate:

/* maximum k-mer length */
#define MAX_KMER 128

I don't know why errors keeps occurring.
Would you please give a piece of tips to fix errors?
Thanks in advance.