-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_12623818-12873304

-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 pasa_asmbl_2247.p1
Valid prediction for HiQ_model.g1276.t1
Valid prediction for GlimmerHMM_glimmerT_1717-T1
Valid prediction for pasa_asmbl_2244.p1
Valid prediction for GlimmerHMM_glimmerT_1726-T1
Valid prediction for Augustus_model.g1263.t1
Valid prediction for CodingQuarry_transcript_2847-T1
Valid prediction for CodingQuarry_transcript_2838-T1
Valid prediction for Augustus_model.g1273.t1
Valid prediction for snap_scaffold_1-snap.2205-T1
Valid prediction for GeneMark_model.2308_t
Valid prediction for snap_scaffold_1-snap.2181-T1
Valid prediction for snap_scaffold_1-snap.2221-T1
Valid prediction for GeneMark_model.2297_t
Valid prediction for CodingQuarry_transcript_2845-T1
Couldn't classify 25492, 25536
Couldn't classify 30095, 30136
Sorry, prediction pasa_asmbl_2780.p1 fails validation.
(TTC)	 GC	25492-25536	GT	AGG
(TTG)	 AG	26253-26352	GT	TGG
(ATG)	 AG	26515-26555	GT	AGG
(GAT)	 AG	26649-26713	GT	AAG
(GGC)	 AG	26920-26968	GT	AGG
(AGG)	 AG	27115-27185	GT	AGG
(GTT)	 AG	27324-27361	GT	AGG
(CTG)	 AG	27455-27480	GT	ATG
(GTC)	 AG	27721-27789	GT	AGG
(ACG)	 AG	30095-30136	TG	CCT
add_exon() Sorry, pasa_asmbl_2780.p1 26515-26555-initial-1 is invalid.
-recovered pasa_asmbl_2780.p1, initial, 26515, 26555
-recovered pasa_asmbl_2780.p1, internal, 26253, 26352
-recovered pasa_asmbl_2780.p1, internal, 26515, 26555
-recovered pasa_asmbl_2780.p1, internal, 26649, 26713
-recovered pasa_asmbl_2780.p1, internal, 26920, 26968
-recovered pasa_asmbl_2780.p1, internal, 27115, 27185
-recovered pasa_asmbl_2780.p1, internal, 27324, 27361
-recovered pasa_asmbl_2780.p1, internal, 27455, 27480
-recovered pasa_asmbl_2780.p1, internal, 27721, 27789
Valid prediction for pasa_asmbl_2230.p1
Valid prediction for GlimmerHMM_glimmerT_1733-T1
Valid prediction for GlimmerHMM_glimmerT_1716-T1
Valid prediction for snap_scaffold_1-snap.2192-T1
Valid prediction for CodingQuarry_transcript_2839-T1
Valid prediction for snap_scaffold_1-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_1714-T1
Couldn't classify 132251, 132291
Sorry, prediction pasa_asmbl_2238.p1 fails validation.
(ATG)	 AC	130134-130224	GT	AGG
(GTA)	 AG	130381-130515	GT	AGG
(GTG)	 AG	130656-130712	GC	CAG
(CCA)	 AG	132251-132291	CT	CCC
-recovered pasa_asmbl_2238.p1, initial, 130134, 130224
add_exon() Sorry, pasa_asmbl_2238.p1 130381-130515-terminal-1 is invalid.
-recovered pasa_asmbl_2238.p1, terminal, 130381, 130515
-recovered pasa_asmbl_2238.p1, internal, 130381, 130515
-recovered pasa_asmbl_2238.p1, internal, 130656, 130712
Valid prediction for GeneMark_model.2280_t
Valid prediction for Augustus_model.g1261.t1
Valid prediction for snap_scaffold_1-snap.2217-T1
Valid prediction for CodingQuarry_transcript_2853-T1
Valid prediction for GeneMark_model.2279_t
Valid prediction for Augustus_model.g1269.t1
Valid prediction for GeneMark_model.2290_t
Valid prediction for snap_scaffold_1-snap.2207-T1
Valid prediction for CodingQuarry_transcript_2846-T1
Valid prediction for HiQ_model.g1285.t1
Valid prediction for GeneMark_model.2288_t
Valid prediction for snap_scaffold_1-snap.2199-T1
Valid prediction for GeneMark_model.2277_t
Valid prediction for CodingQuarry_transcript_2840-T1
Valid prediction for GeneMark_model.2306_t
Couldn't classify 154977, 155162
Sorry, prediction pasa_asmbl_2242.p1 fails validation.
(TTG)	 GG	154977-155162	GT	AGG
(GTC)	 AG	156023-156208	GT	TGG
(ATT)	 AG	156296-156466	GT	AGG
(TGT)	 AG	156557-156646	GT	AAG
(GAG)	 AG	156752-156833	GT	AGG
(GGA)	 AG	157170-157312	GT	AGG
(ACT)	 AG	157431-157508	GT	AGG
(GGT)	 AG	158090-158190	GT	AAG
(GAC)	 AG	158297-158420	GT	AGG
(GGG)	 AG	159053-159229	GT	CAG
(GAT)	 AG	159531-159641	GT	CTG
(GGA)	 AG	159839-159997	AA	AAA
-recovered pasa_asmbl_2242.p1, terminal, 159839, 159997
-recovered pasa_asmbl_2242.p1, internal, 156023, 156208
-recovered pasa_asmbl_2242.p1, internal, 156296, 156466
-recovered pasa_asmbl_2242.p1, internal, 156557, 156646
-recovered pasa_asmbl_2242.p1, internal, 156752, 156833
-recovered pasa_asmbl_2242.p1, internal, 157170, 157312
-recovered pasa_asmbl_2242.p1, internal, 157431, 157508
-recovered pasa_asmbl_2242.p1, internal, 158090, 158190
-recovered pasa_asmbl_2242.p1, internal, 158297, 158420
-recovered pasa_asmbl_2242.p1, internal, 159053, 159229
-recovered pasa_asmbl_2242.p1, internal, 159531, 159641
Valid prediction for pasa_asmbl_2241.p1
Valid prediction for GlimmerHMM_glimmerT_1727-T1
Valid prediction for CodingQuarry_transcript_2855-T1
Valid prediction for pasa_asmbl_2246.p1
Valid prediction for Augustus_model.g1277.t1
Valid prediction for GlimmerHMM_glimmerT_1735-T1
Valid prediction for HiQ_model.g1289.t1
Valid prediction for snap_scaffold_1-snap.2206-T1
Valid prediction for GeneMark_model.2283_t
Couldn't classify 23828, 23860
Sorry, prediction pasa_asmbl_2227.p1 fails validation.
(TTT)	 CT	23828-23860	GT	AGG
(GTT)	 AG	23951-24052	GT	TGG
(ATT)	 AG	24133-24336	GT	GGG
(CAA)	 AG	24468-24572	AA	GAA
-recovered pasa_asmbl_2227.p1, terminal, 24468, 24572
-recovered pasa_asmbl_2227.p1, internal, 23951, 24052
-recovered pasa_asmbl_2227.p1, internal, 24133, 24336
Valid prediction for pasa_asmbl_2245.p1
Valid prediction for snap_scaffold_1-snap.2204-T1
Valid prediction for GlimmerHMM_glimmerT_1739-T1
Valid prediction for GlimmerHMM_glimmerT_1725-T1
Valid prediction for GeneMark_model.2285_t
Valid prediction for Augustus_model.g1266.t1
Valid prediction for GlimmerHMM_glimmerT_1710-T1
Valid prediction for snap_scaffold_1-snap.2188-T1
Valid prediction for Augustus_model.g1275.t1
Valid prediction for snap_scaffold_1-snap.2203-T1
Valid prediction for GeneMark_model.2310_t
Valid prediction for snap_scaffold_1-snap.2194-T1
Valid prediction for Augustus_model.g1288.t1
Valid prediction for Augustus_model.g1268.t1
Valid prediction for snap_scaffold_1-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_1712-T1
Valid prediction for snap_scaffold_1-snap.2183-T1
Couldn't classify 13297, 13437
Sorry, prediction pasa_asmbl_2226.p1 fails validation.
(CGC)	 TG	13297-13437	GT	TGG
(GCC)	 AG	13552-14532	GG	AAG
-recovered pasa_asmbl_2226.p1, terminal, 13552, 14532
Valid prediction for GeneMark_model.2296_t
Valid prediction for snap_scaffold_1-snap.2189-T1
Valid prediction for snap_scaffold_1-snap.2184-T1
Valid prediction for GlimmerHMM_glimmerT_1709-T1
Valid prediction for CodingQuarry_transcript_2854-T1
Valid prediction for GeneMark_model.2299_t

-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 GlimmerHMM_glimmerT_1713-T1
Valid prediction for snap_scaffold_1-snap.2212-T1
Valid prediction for GeneMark_model.2291_t
Valid prediction for Augustus_model.g1284.t1
Valid prediction for Augustus_model.g1274.t1
Valid prediction for snap_scaffold_1-snap.2195-T1
Valid prediction for pasa_asmbl_780.p1
Valid prediction for pasa_asmbl_744.p1
Valid prediction for Augustus_model.g1265.t1
Valid prediction for snap_scaffold_1-snap.2215-T1
Valid prediction for GeneMark_model.2307_t
Valid prediction for snap_scaffold_1-snap.2190-T1
Valid prediction for GeneMark_model.2289_t
Valid prediction for snap_scaffold_1-snap.2210-T1
Valid prediction for CodingQuarry_transcript_2841-T1
Valid prediction for GlimmerHMM_glimmerT_1715-T1
Valid prediction for GeneMark_model.2304_t
Valid prediction for GlimmerHMM_glimmerT_1724-T1
Valid prediction for snap_scaffold_1-snap.2214-T1
Valid prediction for pasa_asmbl_757.p1
Valid prediction for CodingQuarry_transcript_2844-T1
Valid prediction for GeneMark_model.2282_t
Valid prediction for snap_scaffold_1-snap.2196-T1
Valid prediction for GeneMark_model.2281_t
Valid prediction for Augustus_model.g1260.t1
Valid prediction for CodingQuarry_transcript_2843-T1
Valid prediction for pasa_asmbl_777.p1
Valid prediction for HiQ_model.g1278.t1
Valid prediction for CodingQuarry_transcript_2851-T1
Valid prediction for CodingQuarry_transcript_2850-T1
Valid prediction for Augustus_model.g1271.t1
Valid prediction for CodingQuarry_transcript_2836-T1
Valid prediction for GeneMark_model.2294_t
Valid prediction for GlimmerHMM_glimmerT_1720-T1
Valid prediction for GlimmerHMM_glimmerT_1708-T1
Valid prediction for Augustus_model.g1264.t1
Valid prediction for snap_scaffold_1-snap.2211-T1
Valid prediction for GeneMark_model.2301_t
Valid prediction for snap_scaffold_1-snap.2186-T1
Valid prediction for HiQ_model.g1270.t1
Valid prediction for GlimmerHMM_glimmerT_1730-T1
Valid prediction for pasa_asmbl_755.p1
Valid prediction for HiQ_model.g1282.t1
Valid prediction for snap_scaffold_1-snap.2209-T1
Valid prediction for pasa_asmbl_752.p1
Valid prediction for GlimmerHMM_glimmerT_1731-T1
Valid prediction for GeneMark_model.2298_t
Valid prediction for GlimmerHMM_glimmerT_1719-T1
Valid prediction for HiQ_model.g1280.t1
Valid prediction for GlimmerHMM_glimmerT_1736-T1
Valid prediction for snap_scaffold_1-snap.2179-T1
Couldn't classify 232044, 232415
Sorry, prediction pasa_asmbl_749.p1 fails validation.
(GTG)	 CC	232044-232415	CC	TGC
Valid prediction for pasa_asmbl_781.p1
Valid prediction for Augustus_model.g1283.t1
Valid prediction for pasa_asmbl_778.p1
Valid prediction for GeneMark_model.2276_t
Valid prediction for snap_scaffold_1-snap.2208-T1
Valid prediction for CodingQuarry_transcript_2849-T1
Valid prediction for CodingQuarry_transcript_2848-T1
Valid prediction for GeneMark_model.2275_t
Valid prediction for snap_scaffold_1-snap.2216-T1
Valid prediction for GeneMark_model.2293_t
Valid prediction for GeneMark_model.2295_t
Valid prediction for HiQ_model.g1267.t1
Valid prediction for snap_scaffold_1-snap.2185-T1
Valid prediction for snap_scaffold_1-snap.2180-T1
Valid prediction for GlimmerHMM_glimmerT_1729-T1
Valid prediction for GlimmerHMM_glimmerT_1723-T1
Valid prediction for GlimmerHMM_glimmerT_1740-T1
Valid prediction for snap_scaffold_1-snap.2187-T1
Valid prediction for snap_scaffold_1-snap.2200-T1
Valid prediction for CodingQuarry_transcript_2852-T1
Couldn't classify 112428, 112453
Sorry, prediction pasa_asmbl_766.p1 fails validation.
(GCT)	 TC	112428-112453	GT	AGG
(GAT)	 AG	112543-112613	GT	TGG
(GCT)	 AG	112718-112785	GT	AGG
(TAT)	 AG	112898-113053	GT	AGG
(TCT)	 AG	113286-113444	GT	TGG
(AAT)	 AG	113540-113626	GT	GAG
(GGT)	 AG	113831-113950	GT	AAG
(GGT)	 AG	114043-114192	GT	AGG
(CTG)	 AG	114607-114680	GT	TTG
(GCT)	 AG	114778-114931	GT	TGG
(GCT)	 AG	115343-115450	AC	AAA
-recovered pasa_asmbl_766.p1, terminal, 115343, 115450
-recovered pasa_asmbl_766.p1, internal, 112543, 112613
-recovered pasa_asmbl_766.p1, internal, 112718, 112785
-recovered pasa_asmbl_766.p1, internal, 112898, 113053
-recovered pasa_asmbl_766.p1, internal, 113286, 113444
-recovered pasa_asmbl_766.p1, internal, 113540, 113626
-recovered pasa_asmbl_766.p1, internal, 113831, 113950
-recovered pasa_asmbl_766.p1, internal, 114043, 114192
-recovered pasa_asmbl_766.p1, internal, 114607, 114680
-recovered pasa_asmbl_766.p1, internal, 114778, 114931
Valid prediction for GlimmerHMM_glimmerT_1738-T1
Valid prediction for snap_scaffold_1-snap.2222-T1
Valid prediction for HiQ_model.g1259.t1
Valid prediction for GeneMark_model.2305_t
Couldn't classify 72033, 72047
Sorry, prediction pasa_asmbl_776.p1 fails validation.
(ATG)	 CG	68216-68368	GT	AGG
(GAA)	 AG	70048-70125	GT	AGG
(GCT)	 AG	70315-70437	GT	AGG
(TTG)	 AG	70561-70731	GT	TGG
(AAA)	 AG	71135-71260	GT	AGG
(GGT)	 AG	71447-71540	GT	TGG
(TGA)	 AG	71734-71831	GT	CAG
(ATG)	 AG	72033-72047	TG	TGT
-recovered pasa_asmbl_776.p1, initial, 68216, 68368
-recovered pasa_asmbl_776.p1, internal, 70048, 70125
-recovered pasa_asmbl_776.p1, internal, 70315, 70437
-recovered pasa_asmbl_776.p1, internal, 70561, 70731
-recovered pasa_asmbl_776.p1, internal, 71135, 71260
-recovered pasa_asmbl_776.p1, internal, 71447, 71540
-recovered pasa_asmbl_776.p1, internal, 71734, 71831
Valid prediction for GlimmerHMM_glimmerT_1718-T1
Valid prediction for GeneMark_model.2286_t
Valid prediction for snap_scaffold_1-snap.2182-T1
Valid prediction for pasa_asmbl_770.p1
Valid prediction for GeneMark_model.2300_t
Valid prediction for HiQ_model.g1279.t1
Valid prediction for GlimmerHMM_glimmerT_1737-T1
Valid prediction for snap_scaffold_1-snap.2197-T1
Valid prediction for Augustus_model.g1262.t1
Valid prediction for snap_scaffold_1-snap.2201-T1
Valid prediction for snap_scaffold_1-snap.2178-T1
Couldn't classify 232710, 232734
Couldn't classify 233346, 233382
Sorry, prediction pasa_asmbl_748.p1 fails validation.
(GTG)	 CA	232710-232734	GT	AGG
(CGC)	 AG	232846-233037	GT	TGG
(AGG)	 AG	233147-233249	GT	AGG
(CCT)	 AG	233346-233382	GA	CAG
-recovered pasa_asmbl_748.p1, internal, 232846, 233037
-recovered pasa_asmbl_748.p1, internal, 233147, 233249
Valid prediction for HiQ_model.g1272.t1
Valid prediction for snap_scaffold_1-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_1728-T1
Valid prediction for GeneMark_model.2302_t
Valid prediction for GlimmerHMM_glimmerT_1732-T1
Valid prediction for GlimmerHMM_glimmerT_1722-T1
Valid prediction for Augustus_model.g1286.t1
Valid prediction for CodingQuarry_transcript_2842-T1
Valid prediction for pasa_asmbl_774.p1
Valid prediction for GlimmerHMM_glimmerT_1734-T1
Valid prediction for GeneMark_model.2278_t
Valid prediction for GeneMark_model.2303_t
Valid prediction for GlimmerHMM_glimmerT_1711-T1
Valid prediction for snap_scaffold_1-snap.2202-T1
Valid prediction for Augustus_model.g1287.t1
Valid prediction for snap_scaffold_1-snap.2198-T1
Valid prediction for snap_scaffold_1-snap.2191-T1
Valid prediction for GlimmerHMM_glimmerT_1721-T1
Valid prediction for HiQ_model.g1281.t1
Valid prediction for snap_scaffold_1-snap.2218-T1
Valid prediction for GeneMark_model.2287_t
Valid prediction for snap_scaffold_1-snap.2213-T1

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

-building trellis in range 1 - 249487
-exon list size: 571


building trellis

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48.9    
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63.9    
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64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support