Hi,
I ran SOAPsnp on a couple of e_coli read files aligned using SOAPAligner. The size of reference genome is 5.4 MB (http://www.genome.wisc.edu/sequencing/o157.htm).
SOAPsnp is executed with sorted SoapAligner files as input. It ran for more than an hour and the size of the GPFv2 file exceeded 5GB disk space.
Is it a valid execution? Need some info on why does the output file grows that big?
I note that in SOAPsnp website, there is a specification on output file size:
"In text output mode, the output file may be as large as 60 times the genome size". Even then, 5GB is 1000 times bigger than 5.4 MB. Any alternate suggestions to run SOAPsnp?
Cheers,
Gany
I ran SOAPsnp on a couple of e_coli read files aligned using SOAPAligner. The size of reference genome is 5.4 MB (http://www.genome.wisc.edu/sequencing/o157.htm).
SOAPsnp is executed with sorted SoapAligner files as input. It ran for more than an hour and the size of the GPFv2 file exceeded 5GB disk space.
Is it a valid execution? Need some info on why does the output file grows that big?
I note that in SOAPsnp website, there is a specification on output file size:
"In text output mode, the output file may be as large as 60 times the genome size". Even then, 5GB is 1000 times bigger than 5.4 MB. Any alternate suggestions to run SOAPsnp?
Cheers,
Gany
