Hello everybody,

I have a problem with multiz and please I need your help.

I am trying to make a multiple alignment among 20 bird genomes and I am using as reference genome the chicken.

I made the pairwise alignment among each species with the reference genome and I created the chains and nets. After that I converted the nets files into axts and I sorted them and finally converted into maf files. Now I am trying to make the multiple alignment with these maf files by using the roast program. The command that I am running is a typical TBA unix command.

Roast “ the phylogenetic tree” /path_to_the_maf_files/*.maf roast.output.maf

The phylogenetic tree is without the branch lengths and the commas have been replaced with spaces and the ending semi-colon has been removed. The output that I am taking is the following:

grep: chicken.Turkey.sing.maf: No such file or directory
cp: cannot stat `chicken.Mallard.sing.maf': No such file or directory
sh: maf_project: command not found
sh: maf_project: command not found
sh: multiz: command not found
mv: cannot stat`/tmp/_MZ_31826_U1': No such file or directory
mv: cannot stat `/tmp/_MZ_31826_U2': No such file or directory
cp: cannot stat`chicken.Chimney_swift.sing.maf': No such file or directory
roast.v3: command 'cp chicken.Chimney_swift.sing.maf /tmp/_MZ_31826_left.maf2' failed

I am feeling a little bit desperate and I need your help. Thank you very much in advance,

Vasilis