I fail at getting ancestor sequences for my alignment+tree pair using codeml.
My input is an alignment of 25 sequences and associated tree with same ideas.
Alignment seems to be formatted correctly, codeml was complaining at first but
now i think i get the program to start, though in throws the error below. I bet the
problem comes from the formatting of the tree.
the different files i attach are:
codeml.ctl itself , i tried different set of parameters ... let me know which
one help to reconstruct ancestors,
the 2 input files:
test_aa.fa
test.phy_phyml_tree.txt
the output file:
results.out
7 runmode | runmode 0.00
4 seqtype | seqtype 2.00
16 model | model 2.00
20 NSsites | NSsites 0.00
22 icode | icode 0.00
23 Mgene | Mgene 1.00
9 clock | clock 0.00
37 fix_blength | fix_blength 0.00
11 getSE | getSE 1.00
12 RateAncestor | RateAncestor=1 1.00
15 verbose | verbose 0.00
6 cleandata | cleandata 1.00
AAML in paml version 4.9j, October 2019
ns = 25 ls = 130
Reading sequences, sequential format..
Reading seq # 1: genomic
Reading seq # 2: 11816
Reading seq # 3: 5743
Reading seq # 4: 414
Reading seq # 5: 2863
Reading seq # 6: 6316
Reading seq # 7: 1931
Reading seq # 8: 9173
Reading seq # 9: 20557
Reading seq #10: 57247
Reading seq #11: 918
Reading seq #12: 11134
Reading seq #13: 892
Reading seq #14: 81254
Reading seq #15: 8863
Reading seq #16: 15511
Reading seq #17: 10410
Reading seq #18: 19311
Reading seq #19: 12924
Reading seq #20: 14744
Reading seq #21: 24898
Reading seq #22: 108292
Reading seq #23: 6632
Reading seq #24: 30824
Reading seq #25: 13058
Sites with gaps or missing data are removed.
12 ambiguity characters in seq. 1
8 ambiguity characters in seq. 2
8 ambiguity characters in seq. 3
8 ambiguity characters in seq. 4
8 ambiguity characters in seq. 5
8 ambiguity characters in seq. 6
8 ambiguity characters in seq. 7
8 ambiguity characters in seq. 8
8 ambiguity characters in seq. 9
8 ambiguity characters in seq. 10
8 ambiguity characters in seq. 11
8 ambiguity characters in seq. 12
8 ambiguity characters in seq. 13
8 ambiguity characters in seq. 14
8 ambiguity characters in seq. 15
8 ambiguity characters in seq. 16
8 ambiguity characters in seq. 17
8 ambiguity characters in seq. 18
8 ambiguity characters in seq. 19
8 ambiguity characters in seq. 20
8 ambiguity characters in seq. 21
8 ambiguity characters in seq. 22
8 ambiguity characters in seq. 23
8 ambiguity characters in seq. 24
8 ambiguity characters in seq. 25
12 sites are removed. 10 31 32 33 34 60 61 73 107 108 116 117
Sequences read..
Counting site patterns.. 0:00
Compressing, 45 patterns at 118 / 118 sites (100.0%), 0:00
Collecting fpatt[] & pose[], 45 patterns at 118 / 118 sites (100.0%), 0:00
Counting frequencies..
2400 bytes for distance
14400 bytes for conP
2 bytes for fhK
5000000 bytes for space
TREE # 1
(((((((((((15, 13), 2), 20), (18, 23)), 1), 14), (25, 6)), ((22, 21), 24)), ((17, 16), 19)), ((12, (10, 11)), ((7, 8), 9))), 5, (4, 3)); MP score: 36
165600 bytes for conP, adjusted
Reading matrix from jones.dat
error when opening file jones.dat
tell me the full path-name of the file?