Obviously some of your lines don't have valid float data, specifically some line have text id which can't be converted to float.
When you try it in interactive prompt you are trying only first line, so best way is to print the line where you are getting this error and you will know the wrong line e.g.
#!/usr/bin/python
import os,sys
from scipy import stats
import numpy as np
f=open('data2.txt', 'r').readlines()
N=len(f)-1
for i in range(0,N):
w=f[i].split()
l1=w[1:8]
l2=w[8:15]
try:
list1=[float(x) for x in l1]
list2=[float(x) for x in l2]
except ValueError,e:
print "error",e,"on line",i
result=stats.ttest_ind(list1,list2)
print result[1]