parsimony unable to open .tre

Commands in mothur
1

Hello, I am haveing a problem running parsimony and would appreciate any help on this.
Here how it looks like from my end:
“”
mothur > tree.shared(calc=thetayc-jclass, subsample=849)
Using final.pick.an.shared as input file for the shared parameter.
Using 1 processors.
0.03
Output File Names:
final.pick.an.thetayc.0.03.ave.tre
final.pick.an.jclass.0.03.ave.tre
final.pick.an.thetayc.0.03.all.tre
final.pick.an.thetayc.0.03.cons.tre
final.pick.an.jclass.0.03.all.tre
final.pick.an.jclass.0.03.cons.tre

mothur > parsimony(tree=final.pick.an.thetayc.0.03.ave.tre , group=SampleID.design, groups=all)
Unable to open final.pick.an.thetayc.0.03.ave.tre
“”""""
although the file is there and is not being used by any other software.
I thought it might be related to my .design file but i would get this error regardless if i have one stated or not.

my second question on the .design file?
I have 28 samples from 14 animals and two time points (i.e. before and after) and my groups are labeled from G1 to G32 (removed some groups) without any letters .
in my case i can’t compare pairs as there is only one replicate (i.e. similar to the example) !! how can i set my design file to compare before and after for all 8 pairs?
i came up with something like this:
(G1 and G5 are for the same animal i.e. 3447 for before and after i.e. -3 and 9 respectively.)
(again my problem with opening the .tre file is regales whether i provide a .design file or not)


G1 G1_3447_wk-3 G5 G1_3447_wk9 G16 G16_3670_wk-3 G11 G16_3670_wk9 G19 G19_3766_wk-3 G12 G19_3766_wk9 G18 G18_3783_wk-3 G10 G18_3783_wk9 G2 G2_3785_wk-3 G6 G2_3785_wk9 G17 G17_3790_wk-3 G9 G17_3790_wk9 G4 G4_3806_wk-3 G8 G4_3806_wk9 G3 G3_3830_wk-3 G7 G3_3830_wk9 G21 G21_3871_wk-3 G14 G21_3871_wk9 G28 G28_3877_wk-3 G27 G28_3877_wk9 G20 G20_3893_wk-3 G15 G20_3893_wk9 G30 G30_3901_wk-3 G13 G30_3901_wk9 G29 G29_3903_wk-3 G24 G29_3903_wk9 G25 G25_3912_wk-3 G26 G25_3912_wk9 G31 G31_3915_wk-3 G22 G31_3915_wk9 G32 G32_3939_wk-3 G23 G32_3939_wk9
many thanks

O.

2

mothur > parsimony(tree=final.pick.an.thetayc.0.03.ave.tre , group=SampleID.design, groups=all)

It looks like you have a space between the “tre” and the “,”. Can you remove that and try again?

3

thanks, yes it is that space. it runs but i am getting errors regarding the .design file which i need to figure out. (I appreciate your help on)

many many thanks

O.

4

i did this for my .design which is really simple
but this is not comparing pairs within treatment but rather the two pots of samples:
it runs smoothly
sing 1 processors.
********************###########
Comparing to random:||||||||||||||||||||||||||||||||||||||||||||||||||||

Tree# Groups ParsScore ParsSig
1 wk-3-wk9 1 <0.001


Output File Names: final.pick.an.thetayc.0.03.ave.tre.parsimony final.pick.an.thetayc.0.03.ave.tre.psummary
here is the .design file:

G1 wk-3
G5 wk9
G16 wk-3
G11 wk9
G19 wk-3
G12 wk9
G18 wk-3
G10 wk9
G2 wk-3
G6 wk9
G17 wk-3
G9 wk9
G4 wk-3
G8 wk9
G3 wk-3
G7 wk9
G21 wk-3
G14 wk9
G28 wk-3
G27 wk9
G20 wk-3
G15 wk9
G30 wk-3
G13 wk9
G29 wk-3
G24 wk9
G25 wk-3
G26 wk9
G31 wk-3
G22 wk9
G32 wk-3
G23 wk9


many thanks O.
5

If you look at the tree do you have two clear groups - one for wk9 and one for wk-3? The output is saying that your parsimony score is 1, which would indicate two separate groups.

6

Pat, yes there is clear separation. I couldn’t figurer a way to attach a file into my reply but i can email you the pdf.

(however the score for the jclass was 2? what does that mean?? but both had a p value < 0.001)

many thanks

O.

7

It means there are two state changes along the tree. I’d encourage you to look at the treeclimber paper for an explanation of the algorithm:

8

many thanks