condor を用いて PAUP を操作する

2007 年 4 月 11 日 改訂
井上 潤

 このページは condor という Supercomputer の管理システムを用いて PAUP unix version の解析を行うための個人的なメモです.PAUP の unix version に関してはこちらをご覧下さい.


Condor で PAUP を動かし,パラメーターを最尤推定する.
[inoue@phoenix 12tr_b40Noto_fol2]$ cat paup_condor.cmd
# paup running in Condor vanilla Universe

initialdir = /home/inoue/b40Noto_fol/12tr_b40Noto_fol2
Rank = kflops

Executable = /usr/common/i686-linux/bin/paup
Universe = vanilla
requirements = (OpSys =="OSX" && Arch =="PPC") || \
(OpSys =="WINNT51" && Arch =="INTEL") || \
(OpSys =="LINUX" && Arch =="INTEL") || \
(OpSys =="LINUX" && Arch =="ALPHA") || \
(OpSys =="LINUX" && Arch =="X86_64")

should_transfer_files = YES
when_to_transfer_output = ON_EXIT_OR_EVICT
transfer_input_files = paup_12tr_40Noto.nex, Parms_estimate

notification = complete
notify_user = inoue@scs.fsu.edu
arguments = Parms_estimate -n -f
output = EstParms.iout
error = EstParms.error
log = EstParms.log

Queue
[inoue@phoenix 12tr_b40Noto_fol2]$ cat Parms_estimate
#nexus

begin paup;
log file=paup_log;
execute paup_12tr_40Noto.nex; [tree ファイルは seq file の後ろに付けないと動かない]
set crit=likelihood;
lscores 1/nst=6 rmatrix=est basefreq=estimate rates=gamma ncat=8 shape=estimate pinvar=estimate;
end;


Constrain を設定して最尤樹を推定する

[inoue@petal041 Green66Con]$ pwd
/a/fs/guests/users/inoue/paup_dir/NotoCon/32NotoCon/Green66Con[inoue@petal041 Green66Con]$ pwd

#NEXUS

begin paup;
log file=log;
execute Noto32neo12tr;
set crit=likelihood;
lset nst=6 rates=gamma;
loadconstr file=const.tree;
hsearch constraints=Green66ConB enforce=yes;
savetrees file=hser_Green66B.tre replace;
quit;
end;

/a/fs/guests/users/inoue/paup_dir/NotoCon/32NotoCon/Green66Con
const.tree

#NEXUS

BEGIN TREES;

TRANSLATE
1 Scca,
2 Lach,
3 Lame,
4 Leoc,
5 Atsp,
6 Osbi,
7 Pabu,
8 Hial,
9 Gyni,
10 Gnpe,
11 Marc,
12 Xnin,
13 Paco,
14 Noto,
15 Not2,
16 Clop,
17 Chbl,
18 Corn,
19 Nock,
20 Gyki,
21 Anja,
22 Comy,
23 Enja,
24 Same,
25 Cyca,
26 Crla,
27 Cola,
28 Onmy,
29 Sasa,
30 Chag,
31 Pxja,
32 Pama
;
TREE stored_1 = [&R] (1,((2,3),((4,5),((8,(7,(6,((9,(10,11)),((12,13),((14,15),(16,(17,18)))))))),((19,(20,(21,22))),(((23,24),(25,26)),((27,(28,29)),(30,(31,32)))))))));
TREE Green66ConB = [&R] (1,((2,3),((4,5),(((17,16),(6,(7,8)),(18,((9,10),((11,12),(13,(14,15)))))),((19,(20,(21,22))),(((23,24),(25,26)),((27,(28,29)),(30,(31,32)))))))));
TREE Green66Con = [&R] (1,((2,3),((4,5),(((7,6),(9,(10,11)),(8,(((12,(14,15)),13),(16,(17,18))))),((19,(20,(21,22))),(((23,24),(25,26)),((27,(28,29)),(30,(31,32)))))))));
TREE Nel68Con = [&R] (1,(((5,4),(3,2)),(((8,(12,13,14,15,16,17,18)),((9,(10,11)),(7,6))),((((22,21),20),19),(((26,25),(24,23)),(((29,28),27),(30,(31,32))))))));
TREE Green73Con = [&R] (1,((3,2),((5,4),(((8,((12,13,14,15,16,17,18),(9,(10,11)))),(7,6)),((((22,21),20),19),(((26,25),(24,23)),(((29,28),27),(30,(31,32)))))))));
TREE Li_Wil96Con = [&R] (1,((3,2),((5,4),((8,(((9,(10,11)),(12,13,14,15,16,17,18)),(7,6))),((19,(20,(22,21))),(((24,23),(25,26)),((27,(29,28)),(30,(31,32)))))))));
TREE Hil03Con = [&R] (1,((3,2),((5,4),((8,((9,(10,11)),((12,13,14,15,16,17,18),7,6))),((((22,21),20),19),(((26,25),(24,23)),(((29,28),27),(30,(31,32)))))))));
TREE Bon96Con = [&R] (1,((3,2),((5,4),(((8,(12,13,14,15,16,17,18)),(9,(10,11)),(7,6)),((((22,21),20),19),(((26,25),(24,23)),(((29,28),27),(30,(31,32)))))))));
TREE K_N00Con = [&R] (1,((3,2),((5,4),((8,9,(7,(12,13,14,15,16,17,18)),((10,11),6)),((((22,21),20),19),(((26,25),(24,23)),(((29,28),27),(30,(31,32)))))))));

END;



MrBayes などの .tree ファイル (AngTet97_12tr.nex.run3.t) を読みとり,consensus tree を作成する.

以下の Paup block を vi で作成して名前を付けて保存し,PAUP で実行する
ただし,suporting values は tree file に書き出されない.
#NEXUS

begin paup;
execute AngTet97_12tr.nex;
gettrees allblocks=yes StoreTreeWts=yes file=AngTet97_12tr.nex.run3.t mode=3;
contree all/strict=no majrule=yes usetreewts=yes showtree=yes treefile = AngTet97_12tr_Bayes.tre;
end;
* Do you want to "deroot" the tree(s)? (Y/n) は n と答える.Y と答えるとうまく行かない.