-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_210338-475358

-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_18-snap.57-T1
Valid prediction for GlimmerHMM_glimmerT_41641-T1
Valid prediction for GlimmerHMM_glimmerT_41648-T1
Valid prediction for Augustus_model.g27700.t1
Valid prediction for snap_scaffold_18-snap.47-T1
Valid prediction for snap_scaffold_18-snap.60-T1
Couldn't classify 97346, 97403
Couldn't classify 100799, 100852
Sorry, prediction pasa_asmbl_21086.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_21086.p1, internal, 99674, 99892
-recovered pasa_asmbl_21086.p1, internal, 100203, 100270
Couldn't classify 150766, 151004
Sorry, prediction pasa_asmbl_20296.p1 fails validation.
(ATG)	 AC	146067-148083	GT	AGG
(ATC)	 AG	150766-151004	CC	CAC
-recovered pasa_asmbl_20296.p1, initial, 146067, 148083
Valid prediction for Augustus_model.g27703.t1
Couldn't classify 137498, 137513
Sorry, prediction pasa_asmbl_20295.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_20295.p1, initial, 135434, 135455
add_exon() Sorry, pasa_asmbl_20295.p1 136086-136225-initial-1 is invalid.
-recovered pasa_asmbl_20295.p1, initial, 136086, 136225
-recovered pasa_asmbl_20295.p1, internal, 135434, 135455
-recovered pasa_asmbl_20295.p1, internal, 136086, 136225
-recovered pasa_asmbl_20295.p1, internal, 137093, 137176
-recovered pasa_asmbl_20295.p1, internal, 137341, 137393
Valid prediction for CodingQuarry_transcript_23637-T1
Valid prediction for snap_scaffold_18-snap.54-T1
Valid prediction for Augustus_model.g27701.t1
Valid prediction for GlimmerHMM_glimmerT_41651-T1
Valid prediction for GlimmerHMM_glimmerT_41647-T1
Valid prediction for Augustus_model.g27712.t1
Valid prediction for GlimmerHMM_glimmerT_41637-T1
Couldn't classify 7885, 8131
Sorry, prediction pasa_asmbl_20280.p1 fails validation.
(GAG)	 AG	7885-8131	GT	AGG
(ATA)	 AG	9492-9632	GT	AGG
(CCC)	 AG	10056-10102	AA	AGA
-recovered pasa_asmbl_20280.p1, terminal, 10056, 10102
-recovered pasa_asmbl_20280.p1, internal, 7885, 8131
-recovered pasa_asmbl_20280.p1, internal, 9492, 9632
Valid prediction for Augustus_model.g27702.t1
Valid prediction for GlimmerHMM_glimmerT_41642-T1
Valid prediction for HiQ_model.g27692.t1
Valid prediction for snap_scaffold_18-snap.70-T1
Valid prediction for Augustus_model.g27715.t1
Valid prediction for Augustus_model.g27716.t1
Valid prediction for Augustus_model.g27693.t1
Valid prediction for GlimmerHMM_glimmerT_41630-T1
Valid prediction for Augustus_model.g27698.t1
Couldn't classify 101996, 102050
Couldn't classify 104459, 104508
Sorry, prediction pasa_asmbl_21051.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_21051.p1 102395-102604-terminal-1 is invalid.
-recovered pasa_asmbl_21051.p1, terminal, 102395, 102604
-recovered pasa_asmbl_21051.p1, internal, 102395, 102604
-recovered pasa_asmbl_21051.p1, internal, 104459, 104508
Valid prediction for Augustus_model.g27707.t1
Valid prediction for GlimmerHMM_glimmerT_41638-T1
Valid prediction for GlimmerHMM_glimmerT_41635-T1
Valid prediction for HiQ_model.g27705.t1
Valid prediction for snap_scaffold_18-snap.64-T1
Valid prediction for Augustus_model.g27713.t1
Valid prediction for pasa_asmbl_20291.p1
Valid prediction for GlimmerHMM_glimmerT_41626-T1
Valid prediction for snap_scaffold_18-snap.55-T1
Valid prediction for Augustus_model.g27696.t1
Valid prediction for snap_scaffold_18-snap.46-T1
Valid prediction for snap_scaffold_18-snap.59-T1
Valid prediction for snap_scaffold_18-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_41644-T1
Valid prediction for snap_scaffold_18-snap.51-T1
Valid prediction for HiQ_model.g27708.t1
Valid prediction for snap_scaffold_18-snap.61-T1
Valid prediction for Augustus_model.g27706.t1
Couldn't classify 71014, 71047
Sorry, prediction pasa_asmbl_20288.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_20288.p1 75228-75365-initial-1 is invalid.
-recovered pasa_asmbl_20288.p1, initial, 75228, 75365
-recovered pasa_asmbl_20288.p1, terminal, 75228, 75365
-recovered pasa_asmbl_20288.p1, internal, 71772, 71908
-recovered pasa_asmbl_20288.p1, internal, 72524, 72641
-recovered pasa_asmbl_20288.p1, internal, 73688, 73830
-recovered pasa_asmbl_20288.p1, internal, 74376, 74489
-recovered pasa_asmbl_20288.p1, internal, 75228, 75365
Valid prediction for GlimmerHMM_glimmerT_41636-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_18-snap.45-T1
Valid prediction for snap_scaffold_18-snap.67-T1
Valid prediction for GlimmerHMM_glimmerT_41633-T1
Couldn't classify 234880, 235059
Sorry, prediction pasa_asmbl_19568.p1 fails validation.
(GGA)	 CA	234880-235059	GT	CAG
(GAC)	 AG	237433-237600	GT	CAG
(GTG)	 AG	237803-237957	GT	AGG
(GGA)	 AG	238055-238282	GT	AGG
(GCT)	 AG	238363-238499	GT	AGG
(GCC)	 AG	238784-238919	GT	GGG
(GAT)	 AG	239058-239094	TC	AAT
-recovered pasa_asmbl_19568.p1, terminal, 239058, 239094
-recovered pasa_asmbl_19568.p1, internal, 237433, 237600
-recovered pasa_asmbl_19568.p1, internal, 237803, 237957
-recovered pasa_asmbl_19568.p1, internal, 238055, 238282
-recovered pasa_asmbl_19568.p1, internal, 238363, 238499
-recovered pasa_asmbl_19568.p1, internal, 238784, 238919
Valid prediction for Augustus_model.g27704.t1
Valid prediction for pasa_asmbl_19581.p1
Valid prediction for CodingQuarry_transcript_23636-T1
Valid prediction for CodingQuarry_transcript_23640-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 GlimmerHMM_glimmerT_41650-T1
Valid prediction for snap_scaffold_18-snap.44-T1
Valid prediction for HiQ_model.g27709.t1
Valid prediction for GlimmerHMM_glimmerT_41649-T1
Couldn't classify 245611, 245672
Sorry, prediction pasa_asmbl_19564.p1 fails validation.
(TGT)	 CA	245611-245672	GT	TGG
(TCA)	 AG	245989-246073	GT	AGG
(CCA)	 AG	248824-248987	GT	CAG
(GTA)	 AG	249431-249476	AA	AGA
-recovered pasa_asmbl_19564.p1, terminal, 249431, 249476
-recovered pasa_asmbl_19564.p1, internal, 245989, 246073
-recovered pasa_asmbl_19564.p1, internal, 248824, 248987
Valid prediction for CodingQuarry_transcript_23639-T1
Valid prediction for GlimmerHMM_glimmerT_41631-T1
Valid prediction for GlimmerHMM_glimmerT_41652-T1
Valid prediction for CodingQuarry_transcript_23638-T1
Valid prediction for Augustus_model.g27697.t1
Valid prediction for snap_scaffold_18-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_41634-T1
Valid prediction for GlimmerHMM_glimmerT_41640-T1
Valid prediction for Augustus_model.g27711.t1
Valid prediction for snap_scaffold_18-snap.71-T1
Valid prediction for GlimmerHMM_glimmerT_41628-T1
Valid prediction for CodingQuarry_transcript_23634-T1
Valid prediction for HiQ_model.g27714.t1
Valid prediction for snap_scaffold_18-snap.52-T1
Valid prediction for snap_scaffold_18-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_41639-T1
Valid prediction for snap_scaffold_18-snap.66-T1
Valid prediction for Augustus_model.g27710.t1
Valid prediction for GlimmerHMM_glimmerT_41629-T1
Valid prediction for pasa_asmbl_20241.p1
Valid prediction for GlimmerHMM_glimmerT_41643-T1
Valid prediction for snap_scaffold_18-snap.53-T1
Valid prediction for Augustus_model.g27695.t1
Valid prediction for snap_scaffold_18-snap.68-T1
Valid prediction for CodingQuarry_transcript_23635-T1
Valid prediction for Augustus_model.g27699.t1
Valid prediction for snap_scaffold_18-snap.43-T1
Couldn't classify 230051, 230139
Sorry, prediction pasa_asmbl_19573.p1 fails validation.
(ATG)	 GA	219254-219274	GT	AGG
(ATT)	 AG	219676-219921	GT	TGG
(GTA)	 AG	220039-220113	GT	AGG
(CTC)	 AG	221139-221341	GT	AGG
(TGA)	 AG	223009-223089	GT	AGG
(ACT)	 AG	223226-223316	GT	AGG
(GTA)	 AG	225967-226095	GT	AGG
(GAG)	 AG	228053-228137	GT	TGG
(GTG)	 AG	229255-229347	GT	AGG
(AAC)	 AG	230051-230139	GG	ATG
-recovered pasa_asmbl_19573.p1, initial, 219254, 219274
add_exon() Sorry, pasa_asmbl_19573.p1 223009-223089-terminal-1 is invalid.
-recovered pasa_asmbl_19573.p1, terminal, 223009, 223089
add_exon() Sorry, pasa_asmbl_19573.p1 229255-229347-terminal-1 is invalid.
-recovered pasa_asmbl_19573.p1, terminal, 229255, 229347
-recovered pasa_asmbl_19573.p1, internal, 219676, 219921
-recovered pasa_asmbl_19573.p1, internal, 220039, 220113
-recovered pasa_asmbl_19573.p1, internal, 221139, 221341
-recovered pasa_asmbl_19573.p1, internal, 223009, 223089
-recovered pasa_asmbl_19573.p1, internal, 223226, 223316
-recovered pasa_asmbl_19573.p1, internal, 225967, 226095
-recovered pasa_asmbl_19573.p1, internal, 228053, 228137
-recovered pasa_asmbl_19573.p1, internal, 229255, 229347
Valid prediction for Augustus_model.g27694.t1
Valid prediction for snap_scaffold_18-snap.50-T1
Valid prediction for snap_scaffold_18-snap.58-T1
Valid prediction for snap_scaffold_18-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_41625-T1
Valid prediction for GlimmerHMM_glimmerT_41645-T1
Valid prediction for GlimmerHMM_glimmerT_41646-T1
Valid prediction for snap_scaffold_18-snap.62-T1
Valid prediction for GlimmerHMM_glimmerT_41632-T1
Valid prediction for GlimmerHMM_glimmerT_41627-T1

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

-building trellis in range 1 - 265021
-exon list size: 306


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.6    
3.9    
4.2    
4.5    
4.9    
5.2    
5.5    
5.8    
6.2    
6.5    
6.8    
7.1    
7.5    
7.8    
8.1    
8.4    
8.8    
9.1    
9.4    
9.7    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
14.0    
14.3    
14.6    
14.9    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.9    
18.2    
18.5    
18.8    
19.2    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.4    
21.8    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.0    
24.4    
24.7    
25.0    
25.3    
25.6    
26.0    
26.3    
26.6    
26.9    
27.3    
27.6    
27.9    
28.2    
28.6    
28.9    
29.2    
29.5    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.1    
35.4    
35.7    
36.0    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.8    
47.1    
47.4    
47.7    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.3    
52.6    
52.9    
53.2    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
64.0    
64.3    
64.6    
64.9    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.5    
70.8    
71.1    
71.4    
71.8    
72.1    
72.4    
72.7    
73.1    
73.4    
73.7    
74.0    
74.4    
74.7    
75.0    
75.3    
75.6    
76.0    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.2    
78.6    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.8    
81.2    
81.5    
81.8    
82.1    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.1    
85.4    
85.7    
86.0    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.3    
90.6    
90.9    
91.2    
91.6    
91.9    
92.2    
92.5    
92.9    
93.2    
93.5    
93.8    
94.2    
94.5    
94.8    
95.1    
95.5    
95.8    
96.1    
96.4    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 28 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support