ABYSS-P running!

[Fuyou Fu]

Hi all,

I am running ABYSS for assembly my DNA sequencing data. But I donot know why my code is not work. My code is following as : 

mpirun -np 6 ABYSS-P -k 64 -o striga lib='st-1 st-7 st-8 st-9 st-14 st-16' st-1='st-1_R1.fastq.gz st-1_R2.fastq.gz' st-7='st-7_R1.fastq.gz st-7_R2.fastq.gz' st-8='st-8_R1.fastq.gz st-8_R2.fastq.gz' st-9='st-9_R1.fastq.gz st-9_R2.fastq.gz' st-14='st-14_R1.fastq.gz st-14_R2.fastq.gz' st-16='st-16_R1.fastq.gz st-16_R2.fastq.gz'

Thanks,

Fuyou

[Ben Vandervalk]

Hi Fuyou,

The normal way to run ABySS is with the 'abyss-pe' script, e.g.:

$ abyss-pe k=64 name=striga lib='st-1 st-7 st-8 st-9 st-14 st-16' st-1='st-1_R1.fastq.gz st-1_R2.fastq.gz' st-7='st-7_R1.fastq.gz st-7_R2.fastq.gz' st-8='st-8_R1.fastq.gz st-8_R2.fastq.gz' st-9='st-9_R1.fastq.gz st-9_R2.fastq.gz' st-14='st-14_R1.fastq.gz st-14_R2.fastq.gz' st-16='st-16_R1.fastq.gz st-16_R2.fastq.gz'

You don't need to use 'mpirun' command because it is already inside the script (Makefile). For most cluster environments, the value for 'np' is detected automatically from environment variables in your cluster job.  If not, you can explicitly add 'np=6' to the above command.

See the README.md and 'man abyss-pe' for further info.

- Ben

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