-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_6854130-7051096

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_27-snap.1626-T1
Valid prediction for snap_scaffold_27-snap.1628-T1
Valid prediction for CodingQuarry_transcript_41929-T1
Valid prediction for GlimmerHMM_glimmerT_57555-T1
Valid prediction for Augustus_model.g38138.t1
Valid prediction for snap_scaffold_27-snap.1640-T1
Couldn't classify 76801, 76893
Couldn't classify 79672, 79719
Sorry, prediction pasa_asmbl_36421.p1 fails validation.
(AGC)	 CT	76801-76893	GT	ATG
(CTC)	 AG	77861-77922	GT	GGG
(CAT)	 AG	78037-78182	GT	AGG
(ACA)	 AG	78278-78391	GT	AGG
(AGC)	 AG	78754-78928	GT	GAG
(CGG)	 AG	79020-79239	GT	CGG
(GCG)	 AG	79672-79719	GA	TGG
add_exon() Sorry, pasa_asmbl_36421.p1 78754-78928-terminal-3 is invalid.
-recovered pasa_asmbl_36421.p1, terminal, 78754, 78928
-recovered pasa_asmbl_36421.p1, internal, 77861, 77922
-recovered pasa_asmbl_36421.p1, internal, 78037, 78182
-recovered pasa_asmbl_36421.p1, internal, 78278, 78391
-recovered pasa_asmbl_36421.p1, internal, 78754, 78928
-recovered pasa_asmbl_36421.p1, internal, 79020, 79239
Valid prediction for snap_scaffold_27-snap.1633-T1
Valid prediction for Augustus_model.g38130.t1
Couldn't classify 104780, 104947
Sorry, prediction pasa_asmbl_36425.p1 fails validation.
(ATG)	 TC	97654-97812	GT	AGG
(GAG)	 AG	98484-98696	GT	CGG
(GAG)	 AG	98848-98991	GT	TTG
(GTG)	 AG	99223-99459	GT	ACG
(GTG)	 AG	99935-100063	GT	AGG
(GAG)	 AG	102215-102298	GT	AGG
(GCA)	 AG	102742-102861	GT	AGG
(GAG)	 AG	103299-103538	GT	AGG
(TCC)	 AG	104085-104297	GT	CGG
(CTG)	 AG	104430-104612	GT	AGG
(ATC)	 AG	104780-104947	GG	GGG
-recovered pasa_asmbl_36425.p1, initial, 97654, 97812
-recovered pasa_asmbl_36425.p1, internal, 98484, 98696
-recovered pasa_asmbl_36425.p1, internal, 98848, 98991
-recovered pasa_asmbl_36425.p1, internal, 99223, 99459
-recovered pasa_asmbl_36425.p1, internal, 99935, 100063
-recovered pasa_asmbl_36425.p1, internal, 102215, 102298
-recovered pasa_asmbl_36425.p1, internal, 102742, 102861
-recovered pasa_asmbl_36425.p1, internal, 103299, 103538
-recovered pasa_asmbl_36425.p1, internal, 104085, 104297
-recovered pasa_asmbl_36425.p1, internal, 104430, 104612
Valid prediction for CodingQuarry_transcript_41930-T1
Valid prediction for GlimmerHMM_glimmerT_57543-T1
Valid prediction for snap_scaffold_27-snap.1615-T1
Valid prediction for HiQ_model.g38127.t1
Valid prediction for CodingQuarry_transcript_41927-T1
Valid prediction for GlimmerHMM_glimmerT_57544-T1
Valid prediction for GlimmerHMM_glimmerT_57542-T1
Valid prediction for snap_scaffold_27-snap.1619-T1
Valid prediction for snap_scaffold_27-snap.1647-T1
Valid prediction for GlimmerHMM_glimmerT_57535-T1
Valid prediction for snap_scaffold_27-snap.1636-T1
Valid prediction for snap_scaffold_27-snap.1624-T1
Valid prediction for GlimmerHMM_glimmerT_57541-T1
Couldn't classify 79786, 79851
Sorry, prediction pasa_asmbl_36423.p1 fails validation.
(ACC)	 CA	79786-79851	GT	AGG
(AGC)	 AG	79973-80140	GT	AGG
(GAG)	 AG	80222-80366	GT	AGG
(TGA)	 AG	80642-80904	GT	AGG
(GGG)	 AG	81058-81139	GT	GAG
(ATG)	 AG	81373-81503	CC	GAC
add_exon() Sorry, pasa_asmbl_36423.p1 80222-80366-terminal-3 is invalid.
-recovered pasa_asmbl_36423.p1, terminal, 80222, 80366
-recovered pasa_asmbl_36423.p1, terminal, 81373, 81503
-recovered pasa_asmbl_36423.p1, internal, 79973, 80140
-recovered pasa_asmbl_36423.p1, internal, 80222, 80366
-recovered pasa_asmbl_36423.p1, internal, 80642, 80904
-recovered pasa_asmbl_36423.p1, internal, 81058, 81139
Valid prediction for Augustus_model.g38128.t1
Valid prediction for snap_scaffold_27-snap.1611-T1
Valid prediction for Augustus_model.g38139.t1
Valid prediction for snap_scaffold_27-snap.1642-T1
Couldn't classify 73806, 73992
Sorry, prediction pasa_asmbl_36420.p1 fails validation.
(ATG)	 AA	69596-69686	GT	AGG
(CAG)	 AG	70671-73266	GT	AGG
(AGC)	 AG	73806-73992	GA	TGG
-recovered pasa_asmbl_36420.p1, initial, 69596, 69686
-recovered pasa_asmbl_36420.p1, internal, 70671, 73266
Valid prediction for Augustus_model.g38129.t1
Valid prediction for GlimmerHMM_glimmerT_57550-T1
Valid prediction for pasa_asmbl_36416.p1
Valid prediction for snap_scaffold_27-snap.1638-T1
Valid prediction for GlimmerHMM_glimmerT_57546-T1
Valid prediction for snap_scaffold_27-snap.1649-T1
Valid prediction for snap_scaffold_27-snap.1630-T1
Valid prediction for snap_scaffold_27-snap.1622-T1
Valid prediction for snap_scaffold_27-snap.1613-T1
Valid prediction for snap_scaffold_27-snap.1616-T1
Valid prediction for snap_scaffold_27-snap.1620-T1
Valid prediction for CodingQuarry_transcript_41926-T1
Couldn't classify 95758, 95852
Sorry, prediction pasa_asmbl_36424.p1 fails validation.
(ATG)	 TC	91829-91960	GT	TTG
(GCA)	 AG	93806-93877	GT	AGG
(AAA)	 AG	94263-94364	GT	GGG
(TTG)	 AG	94791-94836	GT	AGG
(TTC)	 AG	95012-95108	GT	AGG
(AGA)	 AG	95227-95340	GT	TGG
(GAT)	 AG	95473-95564	GT	AGG
(CTG)	 AG	95758-95852	TT	GGT
-recovered pasa_asmbl_36424.p1, initial, 91829, 91960
add_exon() Sorry, pasa_asmbl_36424.p1 95473-95564-terminal-2 is invalid.
-recovered pasa_asmbl_36424.p1, terminal, 95473, 95564
-recovered pasa_asmbl_36424.p1, internal, 93806, 93877
-recovered pasa_asmbl_36424.p1, internal, 94263, 94364
-recovered pasa_asmbl_36424.p1, internal, 94791, 94836
-recovered pasa_asmbl_36424.p1, internal, 95012, 95108
-recovered pasa_asmbl_36424.p1, internal, 95227, 95340
-recovered pasa_asmbl_36424.p1, internal, 95473, 95564
Valid prediction for snap_scaffold_27-snap.1617-T1
Valid prediction for GlimmerHMM_glimmerT_57540-T1
Valid prediction for GlimmerHMM_glimmerT_57553-T1
Valid prediction for GlimmerHMM_glimmerT_57538-T1
Valid prediction for snap_scaffold_27-snap.1650-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_27-snap.1651-T1
Valid prediction for GlimmerHMM_glimmerT_57539-T1
Valid prediction for snap_scaffold_27-snap.1631-T1
Valid prediction for snap_scaffold_27-snap.1625-T1
Valid prediction for GlimmerHMM_glimmerT_57556-T1
Valid prediction for snap_scaffold_27-snap.1632-T1
Valid prediction for snap_scaffold_27-snap.1643-T1
Valid prediction for snap_scaffold_27-snap.1635-T1
Valid prediction for Augustus_model.g38137.t1
Valid prediction for GlimmerHMM_glimmerT_57548-T1
Valid prediction for GlimmerHMM_glimmerT_57547-T1
Valid prediction for snap_scaffold_27-snap.1637-T1
Valid prediction for Augustus_model.g38131.t1
Valid prediction for snap_scaffold_27-snap.1629-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g38126.t1
Valid prediction for GlimmerHMM_glimmerT_57552-T1
Valid prediction for GlimmerHMM_glimmerT_57545-T1
Valid prediction for Augustus_model.g38133.t1
Valid prediction for snap_scaffold_27-snap.1614-T1
Valid prediction for snap_scaffold_27-snap.1634-T1
Valid prediction for snap_scaffold_27-snap.1641-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57534-T1
Valid prediction for GlimmerHMM_glimmerT_57533-T1
Valid prediction for snap_scaffold_27-snap.1623-T1
Valid prediction for Augustus_model.g38135.t1
Valid prediction for snap_scaffold_27-snap.1618-T1
Valid prediction for GlimmerHMM_glimmerT_57558-T1
Valid prediction for Augustus_model.g38134.t1
Valid prediction for GlimmerHMM_glimmerT_57551-T1
Valid prediction for snap_scaffold_27-snap.1644-T1
Valid prediction for snap_scaffold_27-snap.1648-T1
Valid prediction for Augustus_model.g38136.t1
Valid prediction for snap_scaffold_27-snap.1639-T1
Valid prediction for snap_scaffold_27-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_57549-T1
Valid prediction for GlimmerHMM_glimmerT_57557-T1
Valid prediction for GlimmerHMM_glimmerT_57554-T1
Valid prediction for snap_scaffold_27-snap.1621-T1
Valid prediction for GlimmerHMM_glimmerT_57536-T1
Valid prediction for snap_scaffold_27-snap.1612-T1
Valid prediction for Augustus_model.g38132.t1
Valid prediction for snap_scaffold_27-snap.1652-T1
Valid prediction for snap_scaffold_27-snap.1627-T1
Valid prediction for snap_scaffold_27-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_57537-T1
Valid prediction for snap_scaffold_27-snap.1610-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14182, rend_intergenic: 2405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27108, rend_intergenic: 14399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30121, rend_intergenic: 27134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46363, rend_intergenic: 31266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49192, rend_intergenic: 47787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52828, rend_intergenic: 49473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58450, rend_intergenic: 55009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68250, rend_intergenic: 64738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73270, rend_intergenic: 70664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75018, rend_intergenic: 73661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84273, rend_intergenic: 75356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91774, rend_intergenic: 88460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96110, rend_intergenic: 93463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106497, rend_intergenic: 96592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124472, rend_intergenic: 106652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124562, rend_intergenic: 124515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133462, rend_intergenic: 124962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146450, rend_intergenic: 133794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151707, rend_intergenic: 147685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166886, rend_intergenic: 159724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189603, rend_intergenic: 178013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193719, rend_intergenic: 189705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196967
-exon list size: 410


building trellis

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24.3    
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25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
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26.9    
27.2    
27.4    
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27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.5    
48.8    
49.0    
49.3    
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49.8    
50.0    
50.2    
50.5    
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52.4    
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53.6    
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54.4    
54.6    
54.9    
55.1    
55.3    
55.6    
55.8    
56.1    
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57.3    
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59.0    
59.2    
59.5    
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60.0    
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60.4    
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68.4    
68.7    
68.9    
69.2    
69.4    
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77.2    
77.4    
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78.4    
78.6    
78.9    
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79.4    
79.6    
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80.3    
80.6    
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81.1    
81.3    
81.6    
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82.0    
82.3    
82.5    
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83.3    
83.5    
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84.5    
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86.2    
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86.9    
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87.6    
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88.6    
88.8    
89.1    
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89.6    
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90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
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93.2    
93.4    
93.7    
93.9    
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95.4    
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96.6    
96.8    
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97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 14182, rend_intergenic: 2405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27108, rend_intergenic: 14399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30121, rend_intergenic: 27134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46363, rend_intergenic: 31266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49192, rend_intergenic: 47787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52828, rend_intergenic: 49473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58450, rend_intergenic: 55009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68250, rend_intergenic: 64738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73270, rend_intergenic: 70664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75018, rend_intergenic: 73661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84273, rend_intergenic: 75356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91774, rend_intergenic: 88460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96110, rend_intergenic: 93463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106497, rend_intergenic: 96592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124472, rend_intergenic: 106652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124562, rend_intergenic: 124515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133462, rend_intergenic: 124962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146450, rend_intergenic: 133794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151707, rend_intergenic: 147685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166886, rend_intergenic: 159724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189603, rend_intergenic: 178013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193719, rend_intergenic: 189705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support