Problem running TBA for MSA

[koustavpal]

Hi,

I have alignment data
hg19.panTro3.maf
hg19.gorGor3.maf
hg19.ponAbe2.maf
hg19.calJac3.maf
panTro3.gorGor3.maf
panTro3.ponAbe2.maf
panTro3.calJac3.maf
gorGor3.ponAbe2.maf
gorGor3.calJac3.maf
rheMac2.hg19.maf
rheMac2.panTro3.maf
rheMac2.gorGor3.maf
rheMac2.ponAbe2.maf
rheMac2.calJac3.maf

yet when I run tba with the tree ((((((hg19 panTro3) gorGor3) ponAbe2)) rheMac2) calJac3) it returns error tba.v12 cannot find alignment for hg19 and panTro3 what is it that I am doing wrong? can anyone please explain

[Wallysb01]

Did you ever find an answer to this? I'm having the same issue.

[martinjf]

same problem for me, if anyone could bet what our problem is I would greatly appreciate !

Thanks.

[Wallysb01]

I'm not 100% this is working yet, but after continueing google things, I found this: http://redmine.soe.ucsc.edu/forum/in...609b8e1da196cb

So, I ran roast instead like so:

~/tools/multiz-tba.012109/roast T=/data/walter/tmp E=A "((((A (B C) D) E)(F G))H)" *.*.sing.maf roast.maf

From what I can tell with the tmp files, its doing what I want.

[cariboudoug]

Its possible that the file extension is causing you problems, as indicated by the "X" argument:

X(0) utilize maf files with different suffix from differnt post processing.
0: .sing.maf from single coverage pairwise alignment
1: .toast.maf from full size toast
2: .toast2.maf from reduced size toast

You may want to try switching extension (or running single_cov2 on your files).

Also make sure that the original fasta files used for the pairwise alignments are in your tba directory.