-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_5619740-5903582

-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 GlimmerHMM_glimmerT_55530-T1
Valid prediction for CodingQuarry_transcript_38652-T1
Valid prediction for snap_scaffold_25-snap.1213-T1
Valid prediction for snap_scaffold_25-snap.1232-T1
Valid prediction for CodingQuarry_transcript_38661-T1
Valid prediction for GeneMark_model.96910_t
Valid prediction for snap_scaffold_25-snap.1248-T1
Valid prediction for snap_scaffold_25-snap.1242-T1
Valid prediction for snap_scaffold_25-snap.1244-T1
Valid prediction for Augustus_model.g37066.t1
Valid prediction for GlimmerHMM_glimmerT_55522-T1
Valid prediction for HiQ_model.g37062.t1
Valid prediction for snap_scaffold_25-snap.1258-T1
Valid prediction for GeneMark_model.96941_t
Valid prediction for GlimmerHMM_glimmerT_55524-T1
Valid prediction for snap_scaffold_25-snap.1240-T1
Couldn't classify 20735, 20856
Couldn't classify 23847, 23876
Sorry, prediction pasa_asmbl_33572.p1 fails validation.
(GGG)	 AG	20735-20856	GT	AGG
(TGG)	 AG	21324-21364	GT	AGG
(TGA)	 AG	21463-21587	GT	AGG
(GTG)	 AG	21732-21857	GT	CGG
(TTG)	 AG	22543-22640	GT	TTG
(GAA)	 AG	22826-22925	GT	TGG
(TTT)	 AG	23091-23134	GT	AGG
(CAC)	 AG	23677-23716	GT	AGG
(GAG)	 AG	23847-23876	AG	GGA
add_exon() Sorry, pasa_asmbl_33572.p1 23091-23134-terminal-2 is invalid.
-recovered pasa_asmbl_33572.p1, terminal, 23091, 23134
-recovered pasa_asmbl_33572.p1, internal, 20735, 20856
-recovered pasa_asmbl_33572.p1, internal, 21324, 21364
-recovered pasa_asmbl_33572.p1, internal, 21463, 21587
-recovered pasa_asmbl_33572.p1, internal, 21732, 21857
-recovered pasa_asmbl_33572.p1, internal, 22543, 22640
-recovered pasa_asmbl_33572.p1, internal, 22826, 22925
-recovered pasa_asmbl_33572.p1, internal, 23091, 23134
-recovered pasa_asmbl_33572.p1, internal, 23677, 23716
Valid prediction for Augustus_model.g37040.t1
Valid prediction for snap_scaffold_25-snap.1216-T1
Valid prediction for CodingQuarry_transcript_38657-T1
Valid prediction for snap_scaffold_25-snap.1246-T1
Valid prediction for snap_scaffold_25-snap.1217-T1
Valid prediction for GeneMark_model.96935_t
Couldn't classify 152876, 152951
Sorry, prediction pasa_asmbl_33577.p2 fails validation.
(AGG)	 CC	152876-152951	GT	GGG
(CCT)	 AG	154528-154612	GT	GTG
(AAA)	 AG	154861-154945	GT	AGG
(CTG)	 AG	155114-155242	GT	AGG
(CCA)	 AG	156304-156364	GT	ATG
(TCC)	 AG	156474-156601	GT	AAG
-recovered pasa_asmbl_33577.p2, terminal, 156474, 156601
-recovered pasa_asmbl_33577.p2, internal, 154528, 154612
-recovered pasa_asmbl_33577.p2, internal, 154861, 154945
-recovered pasa_asmbl_33577.p2, internal, 155114, 155242
-recovered pasa_asmbl_33577.p2, internal, 156304, 156364
-recovered pasa_asmbl_33577.p2, internal, 156474, 156601
Valid prediction for GlimmerHMM_glimmerT_55546-T1
Valid prediction for CodingQuarry_transcript_38650-T1
Valid prediction for HiQ_model.g37047.t1
Valid prediction for GeneMark_model.96942_t
Valid prediction for GlimmerHMM_glimmerT_55550-T1
Valid prediction for GeneMark_model.96909_t
Valid prediction for HiQ_model.g37039.t1
Valid prediction for HiQ_model.g37036.t1
Valid prediction for snap_scaffold_25-snap.1255-T1
Valid prediction for snap_scaffold_25-snap.1219-T1
Valid prediction for snap_scaffold_25-snap.1261-T1
Valid prediction for GeneMark_model.96940_t
Valid prediction for GeneMark_model.96937_t
Valid prediction for snap_scaffold_25-snap.1257-T1
Valid prediction for Augustus_model.g37048.t1
Valid prediction for Augustus_model.g37061.t1
Valid prediction for snap_scaffold_25-snap.1243-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_55548-T1
Valid prediction for snap_scaffold_25-snap.1233-T1
Valid prediction for pasa_asmbl_33575.p1
Valid prediction for pasa_asmbl_33568.p1
Couldn't classify 218494, 218553
Sorry, prediction pasa_asmbl_33585.p1 fails validation.
(CCT)	 GT	218494-218553	GT	AGG
(TCT)	 AG	219984-220046	GT	AGG
(CCT)	 AG	220179-220245	GT	GGG
(GCC)	 AG	220403-220476	GT	AGG
(AAT)	 AG	220590-220654	GT	ATG
(GGG)	 AG	220783-220834	GT	CTG
(ATG)	 AG	221084-221119	GT	GGG
(GGA)	 AG	221256-221310	GT	TGG
(ATT)	 AG	221398-221462	GT	ATG
(TTC)	 AG	221743-221821	GT	AGG
(GCT)	 AG	222219-222247	GT	AGG
(AAC)	 AG	222401-222502	GT	ACG
(TAC)	 AG	222724-222753	CC	GAC
-recovered pasa_asmbl_33585.p1, initial, 221084, 221119
add_exon() Sorry, pasa_asmbl_33585.p1 221743-221821-terminal-3 is invalid.
-recovered pasa_asmbl_33585.p1, terminal, 221743, 221821
-recovered pasa_asmbl_33585.p1, terminal, 222724, 222753
-recovered pasa_asmbl_33585.p1, internal, 219984, 220046
-recovered pasa_asmbl_33585.p1, internal, 220179, 220245
-recovered pasa_asmbl_33585.p1, internal, 220403, 220476
-recovered pasa_asmbl_33585.p1, internal, 220590, 220654
-recovered pasa_asmbl_33585.p1, internal, 220783, 220834
-recovered pasa_asmbl_33585.p1, internal, 221084, 221119
-recovered pasa_asmbl_33585.p1, internal, 221256, 221310
-recovered pasa_asmbl_33585.p1, internal, 221398, 221462
-recovered pasa_asmbl_33585.p1, internal, 221743, 221821
-recovered pasa_asmbl_33585.p1, internal, 222219, 222247
-recovered pasa_asmbl_33585.p1, internal, 222401, 222502
Valid prediction for GlimmerHMM_glimmerT_55528-T1
Valid prediction for GeneMark_model.96907_t
Valid prediction for Augustus_model.g37059.t1
Valid prediction for snap_scaffold_25-snap.1252-T1
Valid prediction for GeneMark_model.96920_t
Valid prediction for GeneMark_model.96918_t
Valid prediction for snap_scaffold_25-snap.1231-T1
Valid prediction for GlimmerHMM_glimmerT_55539-T1
Valid prediction for snap_scaffold_25-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_55537-T1
Valid prediction for Augustus_model.g37065.t1
Valid prediction for Augustus_model.g37056.t1
Valid prediction for Augustus_model.g37043.t1
Valid prediction for GeneMark_model.96939_t
Valid prediction for GeneMark_model.96927_t
Valid prediction for GlimmerHMM_glimmerT_55543-T1
Valid prediction for GlimmerHMM_glimmerT_55549-T1
Valid prediction for CodingQuarry_transcript_38656-T1
Valid prediction for snap_scaffold_25-snap.1226-T1
Valid prediction for HiQ_model.g37054.t1
Valid prediction for GeneMark_model.96929_t
Valid prediction for GeneMark_model.96931_t
Couldn't classify 162535, 162691
Sorry, prediction pasa_asmbl_33583.p1 fails validation.
(ACC)	 GG	162535-162691	GT	AGG
(GCG)	 AG	163408-163511	GT	TGG
(ATA)	 AG	163972-164045	GT	AGG
(GGT)	 AG	164189-164259	GT	GGG
(GTG)	 AG	164577-164665	GT	TGG
(ACG)	 AG	164747-164831	GT	TTG
(TGG)	 AG	166837-166946	AG	AGA
-recovered pasa_asmbl_33583.p1, terminal, 166837, 166946
-recovered pasa_asmbl_33583.p1, internal, 163408, 163511
-recovered pasa_asmbl_33583.p1, internal, 163972, 164045
-recovered pasa_asmbl_33583.p1, internal, 164189, 164259
-recovered pasa_asmbl_33583.p1, internal, 164577, 164665
-recovered pasa_asmbl_33583.p1, internal, 164747, 164831
Valid prediction for GlimmerHMM_glimmerT_55517-T1
Valid prediction for GeneMark_model.96919_t
Valid prediction for Augustus_model.g37067.t1
Valid prediction for snap_scaffold_25-snap.1260-T1
Valid prediction for GlimmerHMM_glimmerT_55540-T1
Valid prediction for snap_scaffold_25-snap.1247-T1
Valid prediction for snap_scaffold_25-snap.1239-T1
Valid prediction for GlimmerHMM_glimmerT_55519-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_25-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_55533-T1
Valid prediction for GeneMark_model.96932_t
Valid prediction for pasa_asmbl_34258.p1
Valid prediction for HiQ_model.g37057.t1
Valid prediction for GeneMark_model.96926_t
Valid prediction for snap_scaffold_25-snap.1238-T1
Valid prediction for GlimmerHMM_glimmerT_55536-T1
Couldn't classify 87242, 87315
Sorry, prediction pasa_asmbl_34264.p1 fails validation.
(AAA)	 TG	87242-87315	GT	AGG
(TGC)	 AG	87402-87496	GT	AGG
(GTC)	 AG	87750-87899	GT	AGG
(GTC)	 AG	88019-88105	GT	CGG
(ATG)	 AG	88231-88287	GT	AGG
(AGA)	 AG	88448-88540	GT	AGG
(GGT)	 AG	88841-88898	GT	AGG
(GTA)	 AG	88975-89169	GT	AGG
(GAT)	 AG	89567-89671	GT	AGG
(TCA)	 AG	89771-89823	GT	AGG
(AAT)	 AG	89961-90013	GT	GGG
(AAC)	 AG	90215-90347	GT	TGG
(CTG)	 AG	91467-91576	GT	AGG
(GAC)	 AG	92634-92693	GT	AGG
(CTC)	 AG	92884-93057	AG	GAA
add_exon() Sorry, pasa_asmbl_34264.p1 88231-88287-initial-1 is invalid.
-recovered pasa_asmbl_34264.p1, initial, 88231, 88287
-recovered pasa_asmbl_34264.p1, terminal, 92884, 93057
-recovered pasa_asmbl_34264.p1, internal, 87402, 87496
-recovered pasa_asmbl_34264.p1, internal, 87750, 87899
-recovered pasa_asmbl_34264.p1, internal, 88019, 88105
-recovered pasa_asmbl_34264.p1, internal, 88231, 88287
-recovered pasa_asmbl_34264.p1, internal, 88448, 88540
-recovered pasa_asmbl_34264.p1, internal, 88841, 88898
-recovered pasa_asmbl_34264.p1, internal, 88975, 89169
-recovered pasa_asmbl_34264.p1, internal, 89567, 89671
-recovered pasa_asmbl_34264.p1, internal, 89771, 89823
-recovered pasa_asmbl_34264.p1, internal, 89961, 90013
-recovered pasa_asmbl_34264.p1, internal, 90215, 90347
-recovered pasa_asmbl_34264.p1, internal, 91467, 91576
-recovered pasa_asmbl_34264.p1, internal, 92634, 92693
Valid prediction for snap_scaffold_25-snap.1225-T1
Valid prediction for HiQ_model.g37046.t1
Valid prediction for GlimmerHMM_glimmerT_55520-T1
Valid prediction for Augustus_model.g37051.t1
Valid prediction for Augustus_model.g37058.t1
Valid prediction for GeneMark_model.96928_t
Valid prediction for Augustus_model.g37041.t1
Valid prediction for snap_scaffold_25-snap.1224-T1
Valid prediction for Augustus_model.g37053.t1
Valid prediction for snap_scaffold_25-snap.1214-T1
Valid prediction for snap_scaffold_25-snap.1220-T1
Valid prediction for snap_scaffold_25-snap.1215-T1
Valid prediction for snap_scaffold_25-snap.1234-T1
Valid prediction for GlimmerHMM_glimmerT_55545-T1
Valid prediction for snap_scaffold_25-snap.1245-T1
Valid prediction for snap_scaffold_25-snap.1259-T1
Valid prediction for GlimmerHMM_glimmerT_55531-T1
Valid prediction for GlimmerHMM_glimmerT_55542-T1
Valid prediction for HiQ_model.g37045.t1
Valid prediction for GeneMark_model.96938_t
Valid prediction for GeneMark_model.96934_t
Valid prediction for snap_scaffold_25-snap.1223-T1
Valid prediction for Augustus_model.g37049.t1
Valid prediction for GeneMark_model.96923_t
Valid prediction for Augustus_model.g37064.t1
Valid prediction for Augustus_model.g37063.t1
Valid prediction for GeneMark_model.96921_t
Valid prediction for CodingQuarry_transcript_38651-T1
Valid prediction for snap_scaffold_25-snap.1236-T1
Valid prediction for GeneMark_model.96911_t
Valid prediction for CodingQuarry_transcript_38660-T1
Valid prediction for snap_scaffold_25-snap.1241-T1
Valid prediction for snap_scaffold_25-snap.1253-T1
Valid prediction for HiQ_model.g37038.t1
Valid prediction for GlimmerHMM_glimmerT_55521-T1
Valid prediction for snap_scaffold_25-snap.1222-T1
Valid prediction for GeneMark_model.96933_t
Valid prediction for GeneMark_model.96930_t
Valid prediction for snap_scaffold_25-snap.1221-T1
Valid prediction for snap_scaffold_25-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_55527-T1
Valid prediction for GlimmerHMM_glimmerT_55538-T1
Valid prediction for snap_scaffold_25-snap.1237-T1
Valid prediction for Augustus_model.g37044.t1
Valid prediction for GlimmerHMM_glimmerT_55541-T1
Valid prediction for HiQ_model.g37060.t1
Valid prediction for snap_scaffold_25-snap.1249-T1
Couldn't classify 83146, 84066
Sorry, prediction pasa_asmbl_34265.p1 fails validation.
(AGA)	 TG	83146-84066	AT	GAA
Valid prediction for snap_scaffold_25-snap.1227-T1
Valid prediction for Augustus_model.g37042.t1
Valid prediction for snap_scaffold_25-snap.1250-T1
Valid prediction for pasa_asmbl_34254.p1
Valid prediction for GlimmerHMM_glimmerT_55532-T1
Valid prediction for GeneMark_model.96917_t
Valid prediction for snap_scaffold_25-snap.1230-T1
Valid prediction for pasa_asmbl_34250.p1
Valid prediction for CodingQuarry_transcript_38655-T1
Valid prediction for GlimmerHMM_glimmerT_55547-T1
Valid prediction for GeneMark_model.96908_t
Valid prediction for GlimmerHMM_glimmerT_55523-T1
Valid prediction for GlimmerHMM_glimmerT_55534-T1
Valid prediction for Augustus_model.g37055.t1
Valid prediction for GeneMark_model.96936_t
Valid prediction for GlimmerHMM_glimmerT_55526-T1
Valid prediction for pasa_asmbl_34263.p1
Valid prediction for snap_scaffold_25-snap.1256-T1
Valid prediction for snap_scaffold_25-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_55535-T1
Valid prediction for snap_scaffold_25-snap.1228-T1
Valid prediction for CodingQuarry_transcript_38654-T1
Valid prediction for GlimmerHMM_glimmerT_55525-T1
Valid prediction for GeneMark_model.96912_t
Valid prediction for pasa_asmbl_34267.p1
Valid prediction for GeneMark_model.96925_t
Valid prediction for GlimmerHMM_glimmerT_55544-T1
Valid prediction for CodingQuarry_transcript_38658-T1
Valid prediction for GeneMark_model.96916_t
Valid prediction for GeneMark_model.96922_t
Valid prediction for Augustus_model.g37052.t1
Valid prediction for CodingQuarry_transcript_38659-T1
Couldn't classify 166138, 166204
Sorry, prediction pasa_asmbl_34259.p1 fails validation.
(ACG)	 TG	166138-166204	GT	AGG
(ATC)	 AG	166848-166909	GT	AGG
(GGC)	 AG	167276-167389	GT	AGG
(GTG)	 AG	167614-167815	GT	AGG
(TGC)	 AG	168020-168079	GT	AGG
(ATC)	 AG	168186-168232	TA	GAT
-recovered pasa_asmbl_34259.p1, terminal, 168186, 168232
-recovered pasa_asmbl_34259.p1, internal, 166848, 166909
-recovered pasa_asmbl_34259.p1, internal, 167276, 167389
-recovered pasa_asmbl_34259.p1, internal, 167614, 167815
-recovered pasa_asmbl_34259.p1, internal, 168020, 168079
Valid prediction for GeneMark_model.96914_t
Valid prediction for HiQ_model.g37050.t1
Valid prediction for GlimmerHMM_glimmerT_55529-T1
Valid prediction for HiQ_model.g37037.t1
Valid prediction for GlimmerHMM_glimmerT_55518-T1
Couldn't classify 208743, 209150
Sorry, prediction pasa_asmbl_34253.p1 fails validation.
(CAT)	 TG	208743-209150	TT	GAT
Valid prediction for GeneMark_model.96913_t
Valid prediction for snap_scaffold_25-snap.1251-T1

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

-building trellis in range 1 - 283843
-exon list size: 601


building trellis

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18.7    
18.9    
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22.9    
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23.7    
23.9    
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24.2    
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25.2    
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25.7    
25.9    
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26.2    
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26.9    
27.0    
27.2    
27.4    
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30.5    
30.7    
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56.7    
56.9    
57.0    
57.2    
57.4    
57.5    
57.7    
57.9    
58.0    
58.2    
58.4    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 39 predictions from path traversal

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