(paml) [bsun@login02 psg]$ python3 callcodeml.py phy all.tree
The directory is: /public/home/bsun/bsun/pan-genome/psg/phy
The treeFile is: /public/home/bsun/bsun/pan-genome/psg/all.tree
0%| | 0/1 [00:00<?, ?it/s]
2024-09-19 11:17:21 Starting ModelA null of etnppl_spe ...
Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT
TTC | TCC | TAC | TGC
Leu L TTA | TCA | * TAA | * TGA
TTG | TCG | TAG | Trp W TGG
Leu L CTT | Pro P CCT | His H CAT | Arg R CGT
CTC | CCC | CAC | CGC
CTA | CCA | Gln Q CAA | CGA
CTG | CCG | CAG | CGG
Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT
ATC | ACC | AAC | AGC
ATA | ACA | Lys K AAA | Arg R AGA
Met M ATG | ACG | AAG | AGG
Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT
GTC | GCC | GAC | GGC
GTA | GCA | Glu E GAA | GGA
GTG | GCG | GAG | GGG
Nice code, uuh?
Ambiguity character definition table:
T (1): T
C (1): C
A (1): A
G (1): G
U (1): T
Y (2): T C
R (2): A G
M (2): C A
K (2): T G
S (2): C G
W (2): T A
H (3): T C A
B (3): T C G
V (3): C A G
D (3): T A G
(4): T C A G
N (4): T C A G
? (4): T C A G
ns = 12 ls = 366
Reading sequences, sequential format..
Reading seq # 1: Beaufortia_kweichowensis
Reading seq # 2: Sinocyclocheilus_grahami
Reading seq # 3: Leptobotia_elongata
Reading seq # 4: Oryzias_latipes
Reading seq # 5: Triplophysa_bleekeri
Reading seq # 6: Triplophysa_dalaica
Reading seq # 7: Triplophysa_rosa
Reading seq # 8: Triplophysa_tibetana
Reading seq # 9: Triplophysa_yarkandensis
Reading seq #10: Danio_rerio
Reading seq #11: Ctenopharyngodon_idella
Reading seq #12: Misgurnus_anguillicaudatus
114192 bytes for conP
3744 bytes for fhK
5000000 bytes for space
2 branch types are in tree. Stop if wrong.
TREE # 1
(((10, (11, 2)), ((12, ((((8, (6, 9)), 7), 5), 1)), 3)), 4); MP score: 274
This is a rooted tree, without clock. Check.
Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT
TTC | TCC | TAC | TGC
Leu L TTA | TCA | * TAA | * TGA
TTG | TCG | TAG | Trp W TGG
Leu L CTT | Pro P CCT | His H CAT | Arg R CGT
CTC | CCC | CAC | CGC
CTA | CCA | Gln Q CAA | CGA
CTG | CCG | CAG | CGG
Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT
ATC | ACC | AAC | AGC
ATA | ACA | Lys K AAA | Arg R AGA
Met M ATG | ACG | AAG | AGG
Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT
GTC | GCC | GAC | GGC
GTA | GCA | Glu E GAA | GGA
GTG | GCG | GAG | GGG
Nice code, uuh?
Ambiguity character definition table:
T (1): T
C (1): C
A (1): A
G (1): G
U (1): T
Y (2): T C
R (2): A G
M (2): C A
K (2): T G
S (2): C G
W (2): T A
H (3): T C A
B (3): T C G
V (3): C A G
D (3): T A G
(4): T C A G
N (4): T C A G
? (4): T C A G
ns = 12 ls = 366
Reading sequences, sequential format..
Reading seq # 1: Beaufortia_kweichowensis
Reading seq # 2: Sinocyclocheilus_grahami
Reading seq # 3: Leptobotia_elongata
Reading seq # 4: Oryzias_latipes
Reading seq # 5: Triplophysa_bleekeri
Reading seq # 6: Triplophysa_dalaica
Reading seq # 7: Triplophysa_rosa
Reading seq # 8: Triplophysa_tibetana
Reading seq # 9: Triplophysa_yarkandensis
Reading seq #10: Danio_rerio
Reading seq #11: Ctenopharyngodon_idella
Reading seq #12: Misgurnus_anguillicaudatus
114192 bytes for conP
3744 bytes for fhK
5000000 bytes for space
2 branch types are in tree. Stop if wrong.
TREE # 1
(((10, (11, 2)), ((12, ((((8, (6, 9)), 7), 5), 1)), 3)), 4); MP score: 274
This is a rooted tree, without clock. Check.
2024-09-19 11:19:01 ERROR in running ModelA alte of /public/home/bsun/bsun/pan-genome/psg/phy/etnppl_spe.phy
Error in running codeml for etnppl_spe, skipping.
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [01:39<00:00, 99.86s/it]
Time used: 100.13571500778198 S
有结果出现，还有报错，怎么解决？
(paml) [bsun@login02 psg]$ python3 callcodeml.py phy all.tree The directory is: /public/home/bsun/bsun/pan-genome/psg/phy The treeFile is: /public/home/bsun/bsun/pan-genome/psg/all.tree 0%| | 0/1 [00:00<?, ?it/s] 2024-09-19 11:17:21 Starting ModelA null of etnppl_spe ...
15 verbose | verbose 0.00 7 runmode | runmode 0.00 4 seqtype | seqtype 1.00 13 CodonFreq | CodonFreq 2.00 9 clock | clock 0.00 18 aaDist | aaDist 0.00 16 model | model 2.00 20 NSsites | NSsites 2.00 22 icode | icode 0.00 23 Mgene | Mgene 0.00 24 fix_kappa | fix_kappa 0.00 25 kappa | kappa 2.00 26 fix_omega | fix_omega 1.00 27 omega | omega 1.00 28 fix_alpha | fix_alpha 1.00 29 alpha | alpha 0.00 30 Malpha | Malpha 0.00 31 ncatG | ncatG 3.00 11 getSE | getSE 0.00 12 RateAncestor | RateAncestor 0.00 37 fix_blength | fix_blength 0.00 8 method | method 0.00 36 Small_Diff | Small_Diff 0.00 6 cleandata | cleandata 1.00 CODONML in paml version 4.10.0, September 2020
Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT TTC | TCC | TAC | TGC Leu L TTA | TCA | * TAA | * TGA TTG | TCG | TAG | Trp W TGG
Leu L CTT | Pro P CCT | His H CAT | Arg R CGT CTC | CCC | CAC | CGC CTA | CCA | Gln Q CAA | CGA CTG | CCG | CAG | CGG
Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT ATC | ACC | AAC | AGC ATA | ACA | Lys K AAA | Arg R AGA Met M ATG | ACG | AAG | AGG
Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT GTC | GCC | GAC | GGC GTA | GCA | Glu E GAA | GGA GTG | GCG | GAG | GGG
Nice code, uuh?
Ambiguity character definition table:
T (1): T C (1): C A (1): A G (1): G U (1): T Y (2): T C R (2): A G M (2): C A K (2): T G S (2): C G W (2): T A H (3): T C A B (3): T C G V (3): C A G D (3): T A G
Sequences read.. Counting site patterns.. 0:00 Compressing, 117 patterns at 122 / 122 sites (100.0%), 0:00 Collecting fpatt[] & pose[], 117 patterns at 122 / 122 sites (100.0%), 0:00 Counting codons..
114192 bytes for conP 3744 bytes for fhK 5000000 bytes for space
2 branch types are in tree. Stop if wrong. TREE # 1 (((10, (11, 2)), ((12, ((((8, (6, 9)), 7), 5), 1)), 3)), 4); MP score: 274 This is a rooted tree, without clock. Check.
628056 bytes for conP, adjusted
ntime & nrate & np: 22 2 26
Bounds (np=26): 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 branch=0 freq=0.732186 w0 = 0.203431 branch=0 freq=0.267814 w1 = 1.000000 Qfactor for branch 0 = 8.075058 branch=1 freq=0.582014 w0 = 0.203431 branch=1 freq=0.212885 w1 = 1.000000 branch=1 freq=0.205102 w2 = 1.000000 Qfactor for branch 1 = 7.026725 w[0] = 0.203431 w[1] = 1.000000 w[2] = 1.000000
np = 26 lnL0 = -2001.174772
Iterating by ming2 Initial: fx= 2001.174772 x= 0.01000 0.02107 0.08631 0.02800 0.10029 0.09898 0.04870 0.05759 0.09822 0.02858 0.07388 0.03692 0.03467 0.02362 0.02830 0.08845 0.08165 0.03795 0.07181 0.04940 0.10435 0.05309 2.00000 1.04299 0.03724 0.20343
1 h-m-p 0.0000 0.0003 2162.1961 +++ 1732.815836 m 0.0003 32 | 1/26 2 h-m-p 0.0000 0.0002 311.9341 ++ 1719.676704 m 0.0002 61 | 2/26 3 h-m-p 0.0000 0.0002 696.8072 +YYCCC 1706.412734 4 0.0001 97 | 2/26 4 h-m-p 0.0001 0.0007 135.7781 +YYCCC 1701.682960 4 0.0006 133 | 2/26 5 h-m-p 0.0001 0.0004 78.2489 ++ 1700.717624 m 0.0004 162 | 2/26 6 h-m-p 0.0003 0.0020 102.4822 +YYYYCC 1698.017988 5 0.0011 198 | 2/26 7 h-m-p 0.0002 0.0008 376.8067 +CYCC 1693.604787 3 0.0006 233 | 2/26 8 h-m-p 0.0006 0.0029 278.3854 YCCC 1688.543996 3 0.0012 267 | 2/26 9 h-m-p 0.0019 0.0093 136.0870 CCC 1683.186811 2 0.0025 300 | 2/26 10 h-m-p 0.0008 0.0042 59.1603 CCCC 1682.283803 3 0.0012 335 | 2/26 11 h-m-p 0.0018 0.0090 26.0043 YCC 1682.090547 2 0.0010 367 | 2/26 12 h-m-p 0.0009 0.0045 21.3170 CCCC 1681.956513 3 0.0011 402 | 2/26 13 h-m-p 0.0015 0.0106 14.8208 CCC 1681.838259 2 0.0019 435 | 2/26 14 h-m-p 0.0009 0.0049 31.0115 +CC 1681.401409 1 0.0034 467 | 2/26 15 h-m-p 0.0002 0.0011 62.3878 ++ 1680.980945 m 0.0011 496 | 2/26 16 h-m-p -0.0000 -0.0000 106.0180 h-m-p: -1.89020627e-20 -9.45103137e-20 1.06017996e+02 1680.980945 .. | 2/26 17 h-m-p 0.0000 0.0010 127.1355 ++CYC 1679.998976 2 0.0002 556 | 2/26 18 h-m-p 0.0001 0.0007 99.2235 YCCCC 1678.949019 4 0.0003 592 | 2/26 19 h-m-p 0.0002 0.0016 124.1812 +YCCC 1676.829283 3 0.0006 627 | 2/26 20 h-m-p 0.0001 0.0006 530.4891 +CCC 1671.642835 2 0.0005 661 | 2/26 21 h-m-p 0.0004 0.0019 135.3806 YCCC 1669.788204 3 0.0007 695 | 2/26 22 h-m-p 0.0001 0.0005 104.5115 ++ 1668.504629 m 0.0005 724 | 3/26 23 h-m-p 0.0006 0.0115 72.8985 +YCCC 1667.234016 3 0.0016 759 | 3/26 24 h-m-p 0.0005 0.0025 61.0288 YCCCC 1666.554004 4 0.0011 795 | 3/26 25 h-m-p 0.0016 0.0097 41.9947 YCCC 1666.305684 3 0.0008 829 | 3/26 26 h-m-p 0.0015 0.0173 24.1938 CCC 1666.130284 2 0.0013 862 | 3/26 27 h-m-p 0.0023 0.0308 13.1680 YCCC 1665.837480 3 0.0048 896 | 3/26 28 h-m-p 0.0011 0.0465 56.2550 +CYC 1664.931196 2 0.0039 929 | 3/26 29 h-m-p 0.0046 0.0229 38.6413 YCC 1664.452372 2 0.0031 961 | 3/26 30 h-m-p 0.0088 0.0439 11.6349 CC 1664.369619 1 0.0026 992 | 3/26 31 h-m-p 0.0047 0.0374 6.3947 YC 1664.342546 1 0.0022 1022 | 3/26 32 h-m-p 0.0014 0.1309 9.8860 YC 1664.285294 1 0.0034 1052 | 3/26 33 h-m-p 0.0022 0.0461 15.2972 +YCC 1664.124016 2 0.0063 1085 | 3/26 34 h-m-p 0.0017 0.0409 56.8739 YC 1663.783098 1 0.0037 1115 | 3/26 35 h-m-p 0.0121 0.0822 17.5023 CC 1663.685481 1 0.0036 1146 | 3/26 36 h-m-p 0.0307 0.3920 2.0645 CC 1663.664000 1 0.0088 1177 | 3/26 37 h-m-p 0.0029 0.2187 6.1912 +CCC 1663.537888 2 0.0170 1211 | 3/26 38 h-m-p 0.0042 0.0927 24.8699 CCC 1663.351731 2 0.0064 1244 | 3/26 39 h-m-p 0.0857 1.1152 1.8703 +
2024-09-19 11:18:01 ERROR in running ModelA null of /public/home/bsun/bsun/pan-genome/psg/phy/etnppl_spe.phy
2024-09-19 11:18:01 Starting ModelA alte of etnppl_spe ...
15 verbose | verbose 0.00 7 runmode | runmode 0.00 4 seqtype | seqtype 1.00 13 CodonFreq | CodonFreq 2.00 9 clock | clock 0.00 18 aaDist | aaDist 0.00 16 model | model 2.00 20 NSsites | NSsites 2.00 22 icode | icode 0.00 23 Mgene | Mgene 0.00 24 fix_kappa | fix_kappa 0.00 25 kappa | kappa 2.00 26 fix_omega | fix_omega 0.00 27 omega | omega 2.00 28 fix_alpha | fix_alpha 1.00 29 alpha | alpha 0.00 30 Malpha | Malpha 0.00 31 ncatG | ncatG 3.00 11 getSE | getSE 0.00 12 RateAncestor | RateAncestor 0.00 37 fix_blength | fix_blength 0.00 8 method | method 0.00 36 Small_Diff | Small_Diff 0.00 6 cleandata | cleandata 1.00 CODONML in paml version 4.10.0, September 2020
Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT TTC | TCC | TAC | TGC Leu L TTA | TCA | * TAA | * TGA TTG | TCG | TAG | Trp W TGG
Leu L CTT | Pro P CCT | His H CAT | Arg R CGT CTC | CCC | CAC | CGC CTA | CCA | Gln Q CAA | CGA CTG | CCG | CAG | CGG
Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT ATC | ACC | AAC | AGC ATA | ACA | Lys K AAA | Arg R AGA Met M ATG | ACG | AAG | AGG
Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT GTC | GCC | GAC | GGC GTA | GCA | Glu E GAA | GGA GTG | GCG | GAG | GGG
Nice code, uuh?
Ambiguity character definition table:
T (1): T C (1): C A (1): A G (1): G U (1): T Y (2): T C R (2): A G M (2): C A K (2): T G S (2): C G W (2): T A H (3): T C A B (3): T C G V (3): C A G D (3): T A G
Sequences read.. Counting site patterns.. 0:00 Compressing, 117 patterns at 122 / 122 sites (100.0%), 0:00 Collecting fpatt[] & pose[], 117 patterns at 122 / 122 sites (100.0%), 0:00 Counting codons..
114192 bytes for conP 3744 bytes for fhK 5000000 bytes for space
2 branch types are in tree. Stop if wrong. TREE # 1 (((10, (11, 2)), ((12, ((((8, (6, 9)), 7), 5), 1)), 3)), 4); MP score: 274 This is a rooted tree, without clock. Check.
628056 bytes for conP, adjusted
ntime & nrate & np: 22 3 27
Bounds (np=27): 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 1.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 999.000000 branch=0 freq=0.732186 w0 = 0.203431 branch=0 freq=0.267814 w1 = 1.000000 Qfactor for branch 0 = 8.075058 branch=1 freq=0.582014 w0 = 0.203431 branch=1 freq=0.212885 w1 = 1.000000 branch=1 freq=0.205102 w2 = 3.908910 Qfactor for branch 1 = 4.265088 w[0] = 0.203431 w[1] = 1.000000 w[2] = 3.908910
np = 27 lnL0 = -2005.778699
Iterating by ming2 Initial: fx= 2005.778699 x= 0.01000 0.02107 0.08631 0.02800 0.10029 0.09898 0.04870 0.05759 0.09822 0.02858 0.07388 0.03692 0.03467 0.02362 0.02830 0.08845 0.08165 0.03795 0.07181 0.04940 0.10435 0.05309 2.00000 1.04299 0.03724 0.20343 3.90891
1 h-m-p 0.0000 0.0003 2162.3218 +++ 1737.606227 m 0.0003 33 | 1/27 2 h-m-p 0.0000 0.0002 311.2097 ++ 1724.831466 m 0.0002 63 | 2/27 3 h-m-p 0.0000 0.0002 680.5810 +YYCCC 1711.185530 4 0.0001 100 | 2/27 4 h-m-p 0.0002 0.0009 139.3534 +YYCCC 1706.048478 4 0.0006 137 | 2/27 5 h-m-p 0.0001 0.0004 102.1859 ++ 1704.832769 m 0.0004 167 | 2/27 6 h-m-p 0.0005 0.0023 78.2208 +YCYCCC 1702.249310 5 0.0013 206 | 2/27 7 h-m-p 0.0002 0.0009 359.2215 +CYCC 1696.953016 3 0.0007 242 | 2/27 8 h-m-p 0.0006 0.0029 336.7663 YCCCC 1691.287489 4 0.0011 279 | 2/27 9 h-m-p 0.0011 0.0053 133.1369 YCCC 1686.177637 3 0.0023 314 | 2/27 10 h-m-p 0.0011 0.0054 95.9536 YCCCC 1685.386755 4 0.0007 351 | 2/27 11 h-m-p 0.0006 0.0031 56.0465 CCCC 1684.800130 3 0.0009 387 | 2/27 12 h-m-p 0.0025 0.0156 20.0824 YCC 1684.561286 2 0.0017 420 | 2/27 13 h-m-p 0.0027 0.0215 12.9783 CCC 1684.442233 2 0.0020 454 | 2/27 14 h-m-p 0.0008 0.0123 33.8185 +CCC 1683.862831 2 0.0038 489 | 2/27 15 h-m-p 0.0008 0.0038 69.3598 ++ 1682.578487 m 0.0038 519 | 2/27 16 h-m-p 0.0000 0.0000 110.0413 h-m-p: 3.05262838e-20 1.52631419e-19 1.10041284e+02 1682.578487 .. | 2/27 17 h-m-p 0.0000 0.0010 137.6930 ++YCCC 1681.705284 3 0.0001 583 | 2/27 18 h-m-p 0.0002 0.0008 99.6607 CCCCC 1680.656840 4 0.0003 621 | 2/27 19 h-m-p 0.0002 0.0011 132.5722 YCCCC 1678.580594 4 0.0005 658 | 2/27 20 h-m-p 0.0001 0.0007 509.6396 YCCCC 1675.308018 4 0.0003 695 | 2/27 21 h-m-p 0.0002 0.0008 242.5459 +CYC 1672.380369 2 0.0007 729 | 2/27 22 h-m-p 0.0000 0.0000 160.3447 ++ 1672.131343 m 0.0000 759 | 3/27 23 h-m-p 0.0001 0.0161 44.8568 ++CCC 1670.689346 2 0.0026 795 | 3/27 24 h-m-p 0.0009 0.0044 42.2442 CCCC 1670.215754 3 0.0012 831 | 3/27 25 h-m-p 0.0012 0.0061 29.6347 CCY 1669.957580 2 0.0012 865 | 3/27 26 h-m-p 0.0052 0.0773 6.8769 YCC 1669.890476 2 0.0025 898 | 3/27 27 h-m-p 0.0008 0.0246 20.5176 +CCC 1669.572271 2 0.0038 933 | 3/27 28 h-m-p 0.0025 0.0166 30.7563 CCCC 1669.106000 3 0.0037 969 | 3/27 29 h-m-p 0.0009 0.0160 125.9298 +YCY 1667.980385 2 0.0023 1003 | 3/27 30 h-m-p 0.0016 0.0081 30.0200 CCC 1667.798943 2 0.0018 1037 | 3/27 31 h-m-p 0.0033 0.0245 16.2822 CYC 1667.759623 2 0.0009 1070 | 3/27 32 h-m-p 0.0035 0.9170 4.1879 +++YYC 1665.898183 2 0.1952 1105 | 3/27 33 h-m-p 0.0036 0.0179 113.4535 CCC 1665.155156 2 0.0029 1139 | 3/27 34 h-m-p 0.0013 0.0065 38.2964 YCCC 1665.085844 3 0.0008 1174 | 3/27 35 h-m-p 0.0033 0.0865 9.0187 CC 1665.024485 1 0.0035 1206 | 3/27 36 h-m-p 0.0044 0.3801 7.1837 +YCCC 1664.623202 3 0.0327 1242 | 3/27 37 h-m-p 0.0039 0.0427 60.3312 YCCC 1663.666159 3 0.0090 1277 | 3/27 38 h-m-p 0.0992 0.6686 5.4701 CCCC 1662.871967 3 0.1063 131
2024-09-19 11:19:01 ERROR in running ModelA alte of /public/home/bsun/bsun/pan-genome/psg/phy/etnppl_spe.phy Error in running codeml for etnppl_spe, skipping. 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [01:39<00:00, 99.86s/it] Time used: 100.13571500778198 S