GNUMAP a-to-g running too slow

[Shahar Bracha]

Hi,

I've been trying to run GNUMAP on my fastq  files with the -d flag for a-to-g detection, but it seems to run way too slow. The command I'm using:

gnumap -d -g genome.fa -o filename.output -a .9 -p -v 1 samplename.fastq

 

I'm running it on the ce10 genome (100MB) and my fastqs are around 3GB.

It looks like it's running, but after 2 days it's only [0/0] 1% reads complete.

It's possible that I'm missing something trivial, but I can't find what's wrong. Any help would be greatly appreciated.

 

Thanks,

Shahar.