I am trying to use Siphy (Garber, M. et al, 2009), but am having some difficulties.

I am trying to get the log-odds pi scores for each position in one of the hg18 chromosomes. I used the following command line but the intended output does not seem to be generated:

java -jar bin/scaler_0.5.jar -task 7 -ref hg18 -in chr1.fa -mod primates.mod -minTreeLength 0.5 -out chr1.pi

The command line above results in the following in the terminal:

(((((((hg18:0.006591,)panTro2:0.006639):0.002184,)gorGor1:0.009411):0.009942,)ponAbe2:0.018342):0.014256,)rheMac2:0.036199):0.021496,)calJac1:0.066389):0.056911,)tarSyr1:0.135169):0.011307,)(micMur1:0.091452,)otoGar1:0.128984):0.035463)
base tree total length 0.6507350000000001
Alignment starts at -1 alignment length 247249719

 -3.30858  0.80573  2.63279  0.91909
  0.80573 -4.83099  0.92506  1.90856
  2.63279  0.92506 -6.08850  0.95536
  0.91909  1.90856  0.95536 -2.90928

chr1.pi file is 0 bytes. According to the documentations it's supposed to be a tab limited file with data corresponding to a number of columns.

For your information, I downloaded the hg18 chromosome 1 fasta file from UCSC and the primates.mod from this link (ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/phastCons44way/primates.mod). I have also tried chromosome 1 MAF file and obtained the same results (i.e. no output).