-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_9846212-10101396

-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: +)Couldn't classify 71346, 71410
Couldn't classify 75040, 75093
Sorry, prediction pasa_asmbl_33839.p1 fails validation.
(AGA)	 TC	71346-71410	GT	TTG
(GGA)	 AG	72080-72165	GT	GGG
(TGG)	 AG	74056-74181	GT	CGG
(ATG)	 AG	74288-74382	GT	AGG
(GTA)	 AG	75040-75093	CA	CTC
add_exon() Sorry, pasa_asmbl_33839.p1 74288-74382-initial-1 is invalid.
-recovered pasa_asmbl_33839.p1, initial, 74288, 74382
-recovered pasa_asmbl_33839.p1, internal, 72080, 72165
-recovered pasa_asmbl_33839.p1, internal, 74056, 74181
-recovered pasa_asmbl_33839.p1, internal, 74288, 74382
Valid prediction for GeneMark_model.97845_t
Valid prediction for GeneMark_model.97840_t
Valid prediction for GlimmerHMM_glimmerT_56197-T1
Valid prediction for snap_scaffold_25-snap.2152-T1
Valid prediction for GlimmerHMM_glimmerT_56193-T1
Valid prediction for Augustus_model.g37499.t1
Valid prediction for GlimmerHMM_glimmerT_56191-T1
Couldn't classify 209445, 209549
Couldn't classify 212000, 212160
Sorry, prediction pasa_asmbl_33889.p1 fails validation.
(AAG)	 AG	209445-209549	GT	ATG
(ATG)	 AG	209670-209772	GT	AGG
(GTG)	 AG	212000-212160	GT	AGG
-recovered pasa_asmbl_33889.p1, initial, 209670, 209772
add_exon() Sorry, pasa_asmbl_33889.p1 209670-209772-terminal-3 is invalid.
-recovered pasa_asmbl_33889.p1, terminal, 209670, 209772
-recovered pasa_asmbl_33889.p1, internal, 209445, 209549
-recovered pasa_asmbl_33889.p1, internal, 209670, 209772
-recovered pasa_asmbl_33889.p1, internal, 212000, 212160
Valid prediction for pasa_asmbl_33836.p1
Valid prediction for snap_scaffold_25-snap.2150-T1
Valid prediction for HiQ_model.g37478.t1
Valid prediction for GlimmerHMM_glimmerT_56205-T1
Valid prediction for snap_scaffold_25-snap.2135-T1
Couldn't classify 235247, 235432
Sorry, prediction pasa_asmbl_33847.p1 fails validation.
(ATG)	 AA	233546-233674	GT	AGG
(ACA)	 AG	235247-235432	GG	CTG
-recovered pasa_asmbl_33847.p1, initial, 233546, 233674
Valid prediction for Augustus_model.g37483.t1
Valid prediction for Augustus_model.g37480.t1
Valid prediction for GlimmerHMM_glimmerT_56204-T1
Valid prediction for Augustus_model.g37494.t1
Valid prediction for GlimmerHMM_glimmerT_56189-T1
Valid prediction for snap_scaffold_25-snap.2151-T1
Valid prediction for snap_scaffold_25-snap.2139-T1
Valid prediction for Augustus_model.g37481.t1
Valid prediction for Augustus_model.g37491.t1
Valid prediction for GlimmerHMM_glimmerT_56195-T1
Valid prediction for GeneMark_model.97832_t
Valid prediction for Augustus_model.g37500.t1
Valid prediction for GlimmerHMM_glimmerT_56210-T1
Valid prediction for snap_scaffold_25-snap.2146-T1
Valid prediction for snap_scaffold_25-snap.2144-T1
Valid prediction for Augustus_model.g37488.t1
Valid prediction for GlimmerHMM_glimmerT_56202-T1
Valid prediction for snap_scaffold_25-snap.2157-T1
Valid prediction for CodingQuarry_transcript_38751-T1
Couldn't classify 172411, 172911
Sorry, prediction pasa_asmbl_33842.p1 fails validation.
(TTT)	 TA	172411-172911	CA	GAC
Valid prediction for snap_scaffold_25-snap.2148-T1
Valid prediction for GeneMark_model.97853_t
Valid prediction for GlimmerHMM_glimmerT_56212-T1
Valid prediction for GeneMark_model.97842_t
Valid prediction for GlimmerHMM_glimmerT_56200-T1
Valid prediction for GeneMark_model.97834_t
Valid prediction for Augustus_model.g37497.t1
Valid prediction for Augustus_model.g37487.t1
Valid prediction for GlimmerHMM_glimmerT_56208-T1
Valid prediction for GeneMark_model.97846_t
Couldn't classify 164769, 165485
Sorry, prediction pasa_asmbl_33841.p1 fails validation.
(AGC)	 TC	164769-165485	AG	AGA
Valid prediction for snap_scaffold_25-snap.2137-T1
Valid prediction for GeneMark_model.97830_t
Valid prediction for snap_scaffold_25-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_56207-T1
Valid prediction for GeneMark_model.97835_t
Valid prediction for GeneMark_model.97852_t
Valid prediction for Augustus_model.g37496.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.2142-T1
Valid prediction for Augustus_model.g37479.t1
Valid prediction for GeneMark_model.97854_t
Valid prediction for snap_scaffold_25-snap.2160-T1
Valid prediction for snap_scaffold_25-snap.2155-T1
Valid prediction for snap_scaffold_25-snap.2132-T1
Valid prediction for GeneMark_model.97849_t
Couldn't classify 209876, 209961
Couldn't classify 211614, 211917
Sorry, prediction pasa_asmbl_34497.p1 fails validation.
(CTA)	 CA	209876-209961	GT	AGG
(CAC)	 AG	211614-211917	GA	TGG
Valid prediction for GlimmerHMM_glimmerT_56203-T1
Valid prediction for GeneMark_model.97839_t
Valid prediction for Augustus_model.g37486.t1
Valid prediction for GeneMark_model.97843_t
Valid prediction for snap_scaffold_25-snap.2159-T1
Valid prediction for snap_scaffold_25-snap.2154-T1
Valid prediction for HiQ_model.g37492.t1
Valid prediction for Augustus_model.g37495.t1
Valid prediction for GeneMark_model.97848_t
Valid prediction for GlimmerHMM_glimmerT_56213-T1
Valid prediction for GeneMark_model.97844_t
Valid prediction for Augustus_model.g37489.t1
Valid prediction for snap_scaffold_25-snap.2141-T1
Valid prediction for GlimmerHMM_glimmerT_56194-T1
Valid prediction for GlimmerHMM_glimmerT_56192-T1
Valid prediction for GlimmerHMM_glimmerT_56206-T1
Valid prediction for GlimmerHMM_glimmerT_56190-T1
Valid prediction for GeneMark_model.97837_t
Valid prediction for Augustus_model.g37498.t1
Valid prediction for GlimmerHMM_glimmerT_56198-T1
Valid prediction for snap_scaffold_25-snap.2149-T1
Valid prediction for Augustus_model.g37482.t1
Valid prediction for GlimmerHMM_glimmerT_56199-T1
Couldn't classify 225642, 225770
Couldn't classify 226422, 226595
Sorry, prediction pasa_asmbl_34495.p1 fails validation.
(GAG)	 CA	225642-225770	GT	AGG
(GGT)	 AG	225947-226165	GT	AGG
(GTG)	 AG	226422-226595	GG	CAG
-recovered pasa_asmbl_34495.p1, internal, 225947, 226165
Valid prediction for snap_scaffold_25-snap.2134-T1
Valid prediction for CodingQuarry_transcript_38753-T1
Valid prediction for GeneMark_model.97850_t
Valid prediction for GeneMark_model.97833_t
Valid prediction for HiQ_model.g37493.t1
Valid prediction for CodingQuarry_transcript_38752-T1
Valid prediction for snap_scaffold_25-snap.2138-T1
Couldn't classify 150821, 151013
Sorry, prediction pasa_asmbl_34534.p1 fails validation.
(ATG)	 CC	148466-148468	GT	TGG
(CAT)	 AG	148604-148714	GT	AGG
(AGA)	 AG	150598-150722	GT	TGG
(GGA)	 AG	150821-151013	TC	AGT
-recovered pasa_asmbl_34534.p1, initial, 148466, 148468
-recovered pasa_asmbl_34534.p1, internal, 148604, 148714
-recovered pasa_asmbl_34534.p1, internal, 150598, 150722
Valid prediction for Augustus_model.g37485.t1
Valid prediction for Augustus_model.g37490.t1
Valid prediction for GlimmerHMM_glimmerT_56211-T1
Valid prediction for GlimmerHMM_glimmerT_56209-T1
Valid prediction for pasa_asmbl_34498.p1
Valid prediction for GeneMark_model.97831_t
Valid prediction for Augustus_model.g37484.t1
Valid prediction for snap_scaffold_25-snap.2143-T1
Couldn't classify 57526, 57612
Couldn't classify 57960, 58057
Sorry, prediction pasa_asmbl_34506.p1 fails validation.
(CTC)	 CC	57526-57612	GT	AGG
(GGC)	 AG	57713-57866	GT	TGG
(GCA)	 AG	57960-58057	AG	AGA
-recovered pasa_asmbl_34506.p1, internal, 57713, 57866
Couldn't classify 219029, 219136
Couldn't classify 219349, 219564
Sorry, prediction pasa_asmbl_34545.p1 fails validation.
(AGC)	 AC	219029-219136	GT	ATG
(GTT)	 AG	219349-219564	GT	AGG
-recovered pasa_asmbl_34545.p1, internal, 219349, 219564
Valid prediction for GlimmerHMM_glimmerT_56201-T1
Valid prediction for GeneMark_model.97841_t
Valid prediction for GeneMark_model.97838_t
Valid prediction for GlimmerHMM_glimmerT_56196-T1
Valid prediction for snap_scaffold_25-snap.2156-T1
Valid prediction for snap_scaffold_25-snap.2140-T1
Valid prediction for snap_scaffold_25-snap.2145-T1
Couldn't classify 154099, 154354
Sorry, prediction pasa_asmbl_34500.p1 fails validation.
(CAC)	 TT	154099-154354	GT	AGG
(AAT)	 AG	156730-156813	GT	AGG
(CGG)	 AG	156915-156997	GT	ATG
(GCC)	 AG	157087-157182	GT	GGG
(ATC)	 AG	159098-159203	GT	AGG
(GTC)	 AG	161516-161567	GT	AGG
(AAG)	 AG	162106-162194	GT	ATG
(GGT)	 AG	164218-164306	GT	AAG
(TTA)	 AG	166573-166689	GT	AGG
(AAT)	 AG	166779-166892	GT	AGG
(GTT)	 AG	167934-168021	GT	CCG
(GCA)	 AG	168572-168720	TT	GAT
-recovered pasa_asmbl_34500.p1, terminal, 168572, 168720
-recovered pasa_asmbl_34500.p1, internal, 156730, 156813
-recovered pasa_asmbl_34500.p1, internal, 156915, 156997
-recovered pasa_asmbl_34500.p1, internal, 157087, 157182
-recovered pasa_asmbl_34500.p1, internal, 159098, 159203
-recovered pasa_asmbl_34500.p1, internal, 161516, 161567
-recovered pasa_asmbl_34500.p1, internal, 162106, 162194
-recovered pasa_asmbl_34500.p1, internal, 164218, 164306
-recovered pasa_asmbl_34500.p1, internal, 166573, 166689
-recovered pasa_asmbl_34500.p1, internal, 166779, 166892
-recovered pasa_asmbl_34500.p1, internal, 167934, 168021
Valid prediction for snap_scaffold_25-snap.2133-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.2147-T1
Couldn't classify 205261, 205608
Sorry, prediction pasa_asmbl_34569.p1 fails validation.
(AGA)	 TC	205261-205608	AC	ACA
Valid prediction for GeneMark_model.97847_t
Valid prediction for snap_scaffold_25-snap.2158-T1
Valid prediction for snap_scaffold_25-snap.2153-T1
Sorry, intron length (8) is less than minimum required (10)

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

-building trellis in range 1 - 255185
-exon list size: 325


building trellis

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11.6    
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14.7    
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15.6    
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17.1    
17.4    
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18.3    
18.7    
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19.9    
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20.5    
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21.4    
21.7    
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22.6    
22.9    
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25.1    
25.4    
25.7    
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26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
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30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
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73.1    
73.4    
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74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
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78.0    
78.3    
78.6    
78.9    
79.2    
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80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
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83.5    
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84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support