-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_210338-469528

-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 97346, 97403
Couldn't classify 100799, 100852
Sorry, prediction pasa_asmbl_21093.p1 fails validation.
(TCT)	 CA	97346-97403	GT	GGG
(ACT)	 AG	99674-99892	GT	TTG
(CTT)	 AG	100203-100270	GT	AGG
(TTT)	 AG	100799-100852	GG	GGG
-recovered pasa_asmbl_21093.p1, internal, 99674, 99892
-recovered pasa_asmbl_21093.p1, internal, 100203, 100270
Valid prediction for GlimmerHMM_glimmerT_42594-T1
Valid prediction for snap_scaffold_18-snap.57-T1
Valid prediction for GlimmerHMM_glimmerT_42585-T1
Valid prediction for GlimmerHMM_glimmerT_42582-T1
Valid prediction for Augustus_model.g28470.t1
Couldn't classify 101996, 102050
Couldn't classify 104459, 104508
Sorry, prediction pasa_asmbl_21124.p1 fails validation.
(TTT)	 TG	101996-102050	GT	GGG
(CCA)	 AG	102395-102604	GT	AGG
(ACC)	 AG	104459-104508	GC	ATG
add_exon() Sorry, pasa_asmbl_21124.p1 102395-102604-terminal-1 is invalid.
-recovered pasa_asmbl_21124.p1, terminal, 102395, 102604
-recovered pasa_asmbl_21124.p1, internal, 102395, 102604
-recovered pasa_asmbl_21124.p1, internal, 104459, 104508
Couldn't classify 137498, 137513
Sorry, prediction pasa_asmbl_20320.p1 fails validation.
(ATG)	 AG	135434-135455	GT	AGG
(ATG)	 AG	136086-136225	GT	AGG
(TCA)	 AG	137093-137176	GT	TGG
(GTC)	 AG	137341-137393	GC	AAG
(GAG)	 AG	137498-137513	CT	AGC
-recovered pasa_asmbl_20320.p1, initial, 135434, 135455
add_exon() Sorry, pasa_asmbl_20320.p1 136086-136225-initial-1 is invalid.
-recovered pasa_asmbl_20320.p1, initial, 136086, 136225
-recovered pasa_asmbl_20320.p1, internal, 135434, 135455
-recovered pasa_asmbl_20320.p1, internal, 136086, 136225
-recovered pasa_asmbl_20320.p1, internal, 137093, 137176
-recovered pasa_asmbl_20320.p1, internal, 137341, 137393
Valid prediction for GeneMark_model.73587_t
Valid prediction for snap_scaffold_18-snap.64-T1
Valid prediction for Augustus_model.g28474.t1
Valid prediction for HiQ_model.g28480.t1
Valid prediction for snap_scaffold_18-snap.70-T1
Valid prediction for HiQ_model.g28483.t1
Valid prediction for pasa_asmbl_20316.p1
Couldn't classify 144444, 144510
Couldn't classify 150766, 151004
Sorry, prediction pasa_asmbl_20321.p1 fails validation.
(CAG)	 CC	144444-144510	GT	TGG
(TAT)	 AG	145858-148083	GT	AGG
(ATC)	 AG	150766-151004	CC	CAC
-recovered pasa_asmbl_20321.p1, internal, 145858, 148083
Valid prediction for GeneMark_model.73603_t
Valid prediction for Augustus_model.g28491.t1
Couldn't classify 71014, 71047
Sorry, prediction pasa_asmbl_20314.p1 fails validation.
(ATT)	 CT	71014-71047	GT	AGG
(GAA)	 AG	71772-71908	GT	AGG
(TAT)	 AG	72524-72641	GT	AGG
(AGT)	 AG	73688-73830	GT	CTG
(GAA)	 AG	74376-74489	GT	AGG
(ATG)	 AG	75228-75365	GC	AAG
add_exon() Sorry, pasa_asmbl_20314.p1 75228-75365-initial-1 is invalid.
-recovered pasa_asmbl_20314.p1, initial, 75228, 75365
-recovered pasa_asmbl_20314.p1, terminal, 75228, 75365
-recovered pasa_asmbl_20314.p1, internal, 71772, 71908
-recovered pasa_asmbl_20314.p1, internal, 72524, 72641
-recovered pasa_asmbl_20314.p1, internal, 73688, 73830
-recovered pasa_asmbl_20314.p1, internal, 74376, 74489
-recovered pasa_asmbl_20314.p1, internal, 75228, 75365
Valid prediction for GlimmerHMM_glimmerT_42595-T1
Valid prediction for Augustus_model.g28467.t1
Valid prediction for snap_scaffold_18-snap.60-T1
Valid prediction for GeneMark_model.73593_t
Valid prediction for snap_scaffold_18-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_42599-T1
Valid prediction for GeneMark_model.73606_t
Valid prediction for GlimmerHMM_glimmerT_42592-T1
Valid prediction for GeneMark_model.73592_t
Valid prediction for GeneMark_model.73595_t
Valid prediction for Augustus_model.g28477.t1
Valid prediction for HiQ_model.g28466.t1
Valid prediction for Augustus_model.g28468.t1
Valid prediction for GlimmerHMM_glimmerT_42597-T1
Valid prediction for Augustus_model.g28472.t1
Valid prediction for GlimmerHMM_glimmerT_42581-T1
Valid prediction for GlimmerHMM_glimmerT_42588-T1
Valid prediction for Augustus_model.g28487.t1
Valid prediction for GeneMark_model.73599_t
Valid prediction for GlimmerHMM_glimmerT_42578-T1
Valid prediction for Augustus_model.g28490.t1
Valid prediction for snap_scaffold_18-snap.51-T1
Valid prediction for CodingQuarry_transcript_23591-T1
Valid prediction for GlimmerHMM_glimmerT_42600-T1
Valid prediction for GlimmerHMM_glimmerT_42593-T1
Valid prediction for GlimmerHMM_glimmerT_42586-T1
Couldn't classify 7885, 8131
Sorry, prediction pasa_asmbl_20306.p1 fails validation.
(GAG)	 AG	7885-8131	GT	AGG
(ATA)	 AG	9492-9632	GT	AGG
(CCC)	 AG	10056-10102	AA	AGA
-recovered pasa_asmbl_20306.p1, terminal, 10056, 10102
-recovered pasa_asmbl_20306.p1, internal, 7885, 8131
-recovered pasa_asmbl_20306.p1, internal, 9492, 9632
Valid prediction for GeneMark_model.73607_t
Valid prediction for GeneMark_model.73605_t
Valid prediction for Augustus_model.g28481.t1
Valid prediction for Augustus_model.g28488.t1
Valid prediction for snap_scaffold_18-snap.54-T1
Valid prediction for Augustus_model.g28475.t1
Valid prediction for GlimmerHMM_glimmerT_42598-T1
Valid prediction for GlimmerHMM_glimmerT_42571-T1
Valid prediction for snap_scaffold_18-snap.45-T1
Valid prediction for GlimmerHMM_glimmerT_42574-T1
Valid prediction for GlimmerHMM_glimmerT_42579-T1
Valid prediction for GlimmerHMM_glimmerT_42589-T1
Valid prediction for Augustus_model.g28476.t1
Valid prediction for GeneMark_model.73588_t
Valid prediction for GeneMark_model.73591_t
Valid prediction for Augustus_model.g28482.t1
Valid prediction for snap_scaffold_18-snap.61-T1
Valid prediction for snap_scaffold_18-snap.65-T1
Valid prediction for snap_scaffold_18-snap.46-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 GlimmerHMM_glimmerT_42577-T1
Valid prediction for snap_scaffold_18-snap.66-T1
Valid prediction for snap_scaffold_18-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_42591-T1
Valid prediction for Augustus_model.g28478.t1
Valid prediction for snap_scaffold_18-snap.52-T1
Valid prediction for Augustus_model.g28486.t1
Valid prediction for GlimmerHMM_glimmerT_42584-T1
Valid prediction for GeneMark_model.73598_t
Valid prediction for Augustus_model.g28471.t1
Valid prediction for snap_scaffold_18-snap.55-T1
Valid prediction for GeneMark_model.73586_t
Valid prediction for snap_scaffold_18-snap.42-T1
Valid prediction for snap_scaffold_18-snap.67-T1
Valid prediction for GeneMark_model.73590_t
Valid prediction for CodingQuarry_transcript_23587-T1
Valid prediction for pasa_asmbl_19618.p1
Valid prediction for Augustus_model.g28485.t1
Couldn't classify 229050, 229229
Sorry, prediction pasa_asmbl_19604.p1 fails validation.
(GGA)	 CA	229050-229229	GT	CAG
(GAC)	 AG	231603-231770	GT	CAG
(GTG)	 AG	231973-232127	GT	AGG
(GGA)	 AG	232225-232452	GT	AGG
(GCT)	 AG	232533-232669	GT	AGG
(GCC)	 AG	232954-233089	GT	GGG
(GAT)	 AG	233228-233264	TC	AAT
-recovered pasa_asmbl_19604.p1, terminal, 233228, 233264
-recovered pasa_asmbl_19604.p1, internal, 231603, 231770
-recovered pasa_asmbl_19604.p1, internal, 231973, 232127
-recovered pasa_asmbl_19604.p1, internal, 232225, 232452
-recovered pasa_asmbl_19604.p1, internal, 232533, 232669
-recovered pasa_asmbl_19604.p1, internal, 232954, 233089
Valid prediction for snap_scaffold_18-snap.50-T1
Valid prediction for HiQ_model.g28489.t1
Valid prediction for snap_scaffold_18-snap.43-T1
Valid prediction for Augustus_model.g28479.t1
Valid prediction for CodingQuarry_transcript_23592-T1
Valid prediction for snap_scaffold_18-snap.62-T1
Valid prediction for GlimmerHMM_glimmerT_42590-T1
Valid prediction for GlimmerHMM_glimmerT_42587-T1
Valid prediction for pasa_asmbl_20269.p1
Valid prediction for CodingQuarry_transcript_23593-T1
Valid prediction for snap_scaffold_18-snap.47-T1
Valid prediction for GeneMark_model.73594_t
Valid prediction for snap_scaffold_18-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_42576-T1
Valid prediction for GlimmerHMM_glimmerT_42572-T1
Valid prediction for snap_scaffold_18-snap.48-T1
Valid prediction for snap_scaffold_18-snap.44-T1
Valid prediction for CodingQuarry_transcript_23588-T1
Valid prediction for snap_scaffold_18-snap.53-T1
Valid prediction for GeneMark_model.73600_t
Valid prediction for CodingQuarry_transcript_23594-T1
Valid prediction for Augustus_model.g28473.t1
Valid prediction for GlimmerHMM_glimmerT_42573-T1
Valid prediction for CodingQuarry_transcript_23590-T1
Valid prediction for GlimmerHMM_glimmerT_42596-T1
Valid prediction for CodingQuarry_transcript_23589-T1
Couldn't classify 224221, 224309
Sorry, prediction pasa_asmbl_19607.p1 fails validation.
(ATG)	 GA	213424-213444	GT	AGG
(ATT)	 AG	213846-214091	GT	TGG
(GTA)	 AG	214209-214283	GT	AGG
(CTC)	 AG	215309-215511	GT	AGG
(TGA)	 AG	217179-217259	GT	AGG
(ACT)	 AG	217396-217486	GT	AGG
(GTA)	 AG	220137-220265	GT	AGG
(GAG)	 AG	222223-222307	GT	TGG
(GTG)	 AG	223425-223517	GT	AGG
(AAC)	 AG	224221-224309	GG	ATG
-recovered pasa_asmbl_19607.p1, initial, 213424, 213444
add_exon() Sorry, pasa_asmbl_19607.p1 217179-217259-terminal-1 is invalid.
-recovered pasa_asmbl_19607.p1, terminal, 217179, 217259
add_exon() Sorry, pasa_asmbl_19607.p1 223425-223517-terminal-1 is invalid.
-recovered pasa_asmbl_19607.p1, terminal, 223425, 223517
-recovered pasa_asmbl_19607.p1, internal, 213846, 214091
-recovered pasa_asmbl_19607.p1, internal, 214209, 214283
-recovered pasa_asmbl_19607.p1, internal, 215309, 215511
-recovered pasa_asmbl_19607.p1, internal, 217179, 217259
-recovered pasa_asmbl_19607.p1, internal, 217396, 217486
-recovered pasa_asmbl_19607.p1, internal, 220137, 220265
-recovered pasa_asmbl_19607.p1, internal, 222223, 222307
-recovered pasa_asmbl_19607.p1, internal, 223425, 223517
Valid prediction for Augustus_model.g28469.t1
Valid prediction for GlimmerHMM_glimmerT_42570-T1
Valid prediction for snap_scaffold_18-snap.58-T1
Couldn't classify 239781, 239842
Sorry, prediction pasa_asmbl_19599.p1 fails validation.
(TGT)	 CA	239781-239842	GT	TGG
(TCA)	 AG	240159-240243	GT	AGG
(CCA)	 AG	242994-243157	GT	CAG
(GTA)	 AG	243601-243646	AA	AGA
-recovered pasa_asmbl_19599.p1, terminal, 243601, 243646
-recovered pasa_asmbl_19599.p1, internal, 240159, 240243
-recovered pasa_asmbl_19599.p1, internal, 242994, 243157
Valid prediction for GlimmerHMM_glimmerT_42583-T1
Valid prediction for snap_scaffold_18-snap.68-T1
Valid prediction for snap_scaffold_18-snap.69-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.56-T1
Valid prediction for GeneMark_model.73589_t
Valid prediction for GlimmerHMM_glimmerT_42575-T1
Valid prediction for HiQ_model.g28484.t1
Valid prediction for GeneMark_model.73596_t
Valid prediction for GeneMark_model.73601_t
Valid prediction for GlimmerHMM_glimmerT_42580-T1

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

-building trellis in range 1 - 259191
-exon list size: 378


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 242546 - 259191
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support