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Old 01-13-2014, 04:37 AM   #1
syintel87
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Join Date: Dec 2012
Posts: 81
Default [Abyss de novo assembly] setting 127 k-mer length

"How to set kmer length as 127?"

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

1. The codes below gave errors.
Quote:
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.
Quote:
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.
Quote:
/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.
Quote:
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:
Quote:
/* 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.
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