-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_16284308-16487279

-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 Augustus_model.g21015.t1
Valid prediction for GlimmerHMM_glimmerT_31475-T1
Valid prediction for GeneMark_model.54280_t
Valid prediction for snap_scaffold_12-snap.3158-T1
Valid prediction for Augustus_model.g21014.t1
Couldn't classify 72873, 72982
Couldn't classify 73099, 73297
Sorry, prediction pasa_asmbl_9171.p1 fails validation.
(GGA)	 TA	72873-72982	GT	AGG
(GGG)	 AG	73099-73297	GC	AGG
-recovered pasa_asmbl_9171.p1, internal, 73099, 73297
Valid prediction for snap_scaffold_12-snap.3194-T1
Couldn't classify 49905, 49978
Couldn't classify 55407, 55553
Sorry, prediction pasa_asmbl_9125.p1 fails validation.
(GGT)	 TA	49905-49978	GT	CGG
(GAT)	 AG	51013-51146	GT	AGG
(AAG)	 AG	51289-51465	GT	AGG
(TGG)	 AG	53613-53730	GT	AGG
(ATC)	 AG	54014-54113	GT	AGG
(AGT)	 AG	54439-54651	GT	AGG
(ACT)	 AG	54797-54938	GT	CGG
(GAG)	 AG	55067-55176	GT	AGG
(GTT)	 AG	55407-55553	GT	AGG
-recovered pasa_asmbl_9125.p1, internal, 51013, 51146
-recovered pasa_asmbl_9125.p1, internal, 51289, 51465
-recovered pasa_asmbl_9125.p1, internal, 53613, 53730
-recovered pasa_asmbl_9125.p1, internal, 54014, 54113
-recovered pasa_asmbl_9125.p1, internal, 54439, 54651
-recovered pasa_asmbl_9125.p1, internal, 54797, 54938
-recovered pasa_asmbl_9125.p1, internal, 55067, 55176
-recovered pasa_asmbl_9125.p1, internal, 55407, 55553
Valid prediction for HiQ_model.g21012.t1
Valid prediction for snap_scaffold_12-snap.3162-T1
Valid prediction for Augustus_model.g21019.t1
Valid prediction for snap_scaffold_12-snap.3186-T1
Valid prediction for GlimmerHMM_glimmerT_31485-T1
Valid prediction for GlimmerHMM_glimmerT_31467-T1
Valid prediction for GlimmerHMM_glimmerT_31473-T1
Valid prediction for GlimmerHMM_glimmerT_31466-T1
Valid prediction for snap_scaffold_12-snap.3161-T1
Valid prediction for GlimmerHMM_glimmerT_31476-T1
Valid prediction for CodingQuarry_transcript_10492-T1
Valid prediction for GeneMark_model.54290_t
Valid prediction for GlimmerHMM_glimmerT_31479-T1
Valid prediction for snap_scaffold_12-snap.3193-T1
Valid prediction for GeneMark_model.54283_t
Valid prediction for GlimmerHMM_glimmerT_31478-T1
Valid prediction for pasa_asmbl_9151.p1
Valid prediction for Augustus_model.g21008.t1
Valid prediction for Augustus_model.g21004.t1
Valid prediction for snap_scaffold_12-snap.3179-T1
Valid prediction for snap_scaffold_12-snap.3167-T1
Valid prediction for snap_scaffold_12-snap.3189-T1
Valid prediction for snap_scaffold_12-snap.3187-T1
Valid prediction for GeneMark_model.54275_t
Valid prediction for Augustus_model.g21020.t1
Valid prediction for Augustus_model.g20994.t1
Valid prediction for GeneMark_model.54286_t
Valid prediction for Augustus_model.g21006.t1
Valid prediction for GeneMark_model.54282_t
Valid prediction for pasa_asmbl_9134.p1
Valid prediction for GlimmerHMM_glimmerT_31464-T1
Valid prediction for CodingQuarry_transcript_10491-T1
Valid prediction for GlimmerHMM_glimmerT_31461-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.3170-T1
Couldn't classify 62483, 62578
Sorry, prediction pasa_asmbl_9128.p1 fails validation.
(ATG)	 TC	58928-59027	GT	AGG
(GTC)	 AG	59858-59995	GT	GTG
(ACC)	 AG	60927-61102	GT	AGG
(AGA)	 AG	61826-61943	GT	TGG
(GTG)	 AG	62208-62338	GT	AGG
(GGA)	 AG	62483-62578	TA	GGT
-recovered pasa_asmbl_9128.p1, initial, 58928, 59027
-recovered pasa_asmbl_9128.p1, internal, 59858, 59995
-recovered pasa_asmbl_9128.p1, internal, 60927, 61102
-recovered pasa_asmbl_9128.p1, internal, 61826, 61943
-recovered pasa_asmbl_9128.p1, internal, 62208, 62338
Valid prediction for GeneMark_model.54292_t
Valid prediction for HiQ_model.g21010.t1
Valid prediction for GeneMark_model.54296_t
Couldn't classify 128487, 128681
Couldn't classify 131234, 131413
Sorry, prediction pasa_asmbl_9142.p1 fails validation.
(GCT)	 GA	128487-128681	GT	ATG
(GTG)	 AG	129808-129948	GT	AGG
(GTT)	 AG	130161-130261	GT	AGG
(AAT)	 AG	130763-130916	GT	AGG
(GAC)	 AG	131030-131131	GT	AGG
(ATT)	 AG	131234-131413	GT	AGG
add_exon() Sorry, pasa_asmbl_9142.p1 130161-130261-terminal-2 is invalid.
-recovered pasa_asmbl_9142.p1, terminal, 130161, 130261
-recovered pasa_asmbl_9142.p1, internal, 129808, 129948
-recovered pasa_asmbl_9142.p1, internal, 130161, 130261
-recovered pasa_asmbl_9142.p1, internal, 130763, 130916
-recovered pasa_asmbl_9142.p1, internal, 131030, 131131
-recovered pasa_asmbl_9142.p1, internal, 131234, 131413
Valid prediction for snap_scaffold_12-snap.3169-T1
Valid prediction for snap_scaffold_12-snap.3163-T1
Couldn't classify 21395, 21442
Sorry, prediction GeneMark_model.54270_t fails validation.
(GCA)	 AG	21395-21442	GT	CTG
(GTG)	 AG	21487-22167	GT	GAG
(CAA)	 AG	22245-22521	GG	AAG
add_exon() Sorry, GeneMark_model.54270_t 21487-22167-terminal-1 is invalid.
-recovered GeneMark_model.54270_t, terminal, 21487, 22167
-recovered GeneMark_model.54270_t, terminal, 22245, 22521
-recovered GeneMark_model.54270_t, internal, 21395, 21442
-recovered GeneMark_model.54270_t, internal, 21487, 22167
Valid prediction for snap_scaffold_12-snap.3181-T1
Valid prediction for Augustus_model.g21000.t1
Valid prediction for snap_scaffold_12-snap.3171-T1
Valid prediction for GlimmerHMM_glimmerT_31474-T1
Valid prediction for snap_scaffold_12-snap.3192-T1
Valid prediction for snap_scaffold_12-snap.3191-T1
Valid prediction for snap_scaffold_12-snap.3173-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g21017.t1
Valid prediction for GeneMark_model.54278_t
Valid prediction for Augustus_model.g21009.t1
Valid prediction for GeneMark_model.54293_t
Valid prediction for CodingQuarry_transcript_10496-T1
Valid prediction for GlimmerHMM_glimmerT_31462-T1
Valid prediction for GlimmerHMM_glimmerT_31459-T1
Valid prediction for CodingQuarry_transcript_10493-T1
Valid prediction for snap_scaffold_12-snap.3176-T1
Valid prediction for GeneMark_model.54281_t
Valid prediction for CodingQuarry_transcript_10494-T1
Valid prediction for GeneMark_model.54269_t
Valid prediction for GeneMark_model.54273_t
Valid prediction for snap_scaffold_12-snap.3182-T1
Valid prediction for HiQ_model.g21001.t1
Valid prediction for GeneMark_model.54267_t
Valid prediction for snap_scaffold_12-snap.3166-T1
Valid prediction for GeneMark_model.54291_t
Valid prediction for GlimmerHMM_glimmerT_31457-T1
Valid prediction for Augustus_model.g20991.t1
Valid prediction for GlimmerHMM_glimmerT_31480-T1
Valid prediction for GlimmerHMM_glimmerT_31482-T1
Valid prediction for snap_scaffold_12-snap.3174-T1
Couldn't classify 44299, 44324
Couldn't classify 44805, 46839
Sorry, prediction pasa_asmbl_9124.p1 fails validation.
(ACA)	 AC	44299-44324	GT	AGG
(GTG)	 AG	44805-46839	GG	GAG
Valid prediction for Augustus_model.g20996.t1
Valid prediction for snap_scaffold_12-snap.3164-T1
Valid prediction for HiQ_model.g21013.t1
Valid prediction for Augustus_model.g21018.t1
Valid prediction for pasa_asmbl_9129.p1
Valid prediction for snap_scaffold_12-snap.3165-T1
Valid prediction for snap_scaffold_12-snap.3175-T1
Valid prediction for Augustus_model.g20992.t1
Valid prediction for GlimmerHMM_glimmerT_31481-T1
Valid prediction for GeneMark_model.54274_t
Valid prediction for Augustus_model.g21023.t1
Couldn't classify 67535, 67676
Couldn't classify 68201, 68300
Sorry, prediction pasa_asmbl_9160.p1 fails validation.
(AGG)	 GC	67535-67676	GT	AGG
(CAC)	 AG	67834-67987	GT	GTG
(TTT)	 AG	68201-68300	GG	AAG
-recovered pasa_asmbl_9160.p1, internal, 67834, 67987
Valid prediction for snap_scaffold_12-snap.3185-T1
Valid prediction for Augustus_model.g21005.t1
Valid prediction for GlimmerHMM_glimmerT_31468-T1
Valid prediction for GeneMark_model.54287_t
Valid prediction for GlimmerHMM_glimmerT_31471-T1
Valid prediction for CodingQuarry_transcript_10495-T1
Valid prediction for Augustus_model.g20999.t1
Valid prediction for Augustus_model.g21003.t1
Valid prediction for CodingQuarry_transcript_10490-T1
Valid prediction for GeneMark_model.54284_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 snap_scaffold_12-snap.3188-T1
Valid prediction for snap_scaffold_12-snap.3190-T1
Valid prediction for GlimmerHMM_glimmerT_31456-T1
Valid prediction for snap_scaffold_12-snap.3157-T1
Valid prediction for snap_scaffold_12-snap.3168-T1
Valid prediction for GlimmerHMM_glimmerT_31465-T1
Valid prediction for GeneMark_model.54268_t
Valid prediction for GlimmerHMM_glimmerT_31477-T1
Valid prediction for GlimmerHMM_glimmerT_31458-T1
Valid prediction for snap_scaffold_12-snap.3156-T1
Valid prediction for Augustus_model.g21022.t1
Valid prediction for GeneMark_model.54288_t
Valid prediction for GlimmerHMM_glimmerT_31460-T1
Valid prediction for Augustus_model.g20989.t1
Valid prediction for Augustus_model.g21002.t1
Valid prediction for GeneMark_model.54266_t
Valid prediction for GlimmerHMM_glimmerT_31472-T1
Valid prediction for Augustus_model.g20995.t1
Valid prediction for GlimmerHMM_glimmerT_31484-T1
Valid prediction for snap_scaffold_12-snap.3172-T1
Valid prediction for Augustus_model.g20990.t1
Valid prediction for Augustus_model.g21007.t1
Valid prediction for snap_scaffold_12-snap.3180-T1
Valid prediction for snap_scaffold_12-snap.3154-T1
Valid prediction for GlimmerHMM_glimmerT_31470-T1
Valid prediction for GeneMark_model.54294_t
Valid prediction for snap_scaffold_12-snap.3183-T1
Valid prediction for GlimmerHMM_glimmerT_31463-T1
Valid prediction for snap_scaffold_12-snap.3155-T1
Valid prediction for Augustus_model.g21016.t1
Valid prediction for snap_scaffold_12-snap.3159-T1
Valid prediction for snap_scaffold_12-snap.3178-T1
Valid prediction for Augustus_model.g21021.t1
Valid prediction for snap_scaffold_12-snap.3177-T1
Valid prediction for GlimmerHMM_glimmerT_31469-T1
Valid prediction for HiQ_model.g20997.t1
Valid prediction for snap_scaffold_12-snap.3184-T1
Valid prediction for GeneMark_model.54285_t
Valid prediction for Augustus_model.g20998.t1
Valid prediction for CodingQuarry_transcript_10489-T1
Valid prediction for Augustus_model.g20993.t1
Valid prediction for snap_scaffold_12-snap.3160-T1
Valid prediction for Augustus_model.g21011.t1
Couldn't classify 21428, 22879
Sorry, prediction pasa_asmbl_8264.p1 fails validation.
(TCT)	 TG	21428-22879	AG	CGA
Valid prediction for GlimmerHMM_glimmerT_31483-T1
Valid prediction for GeneMark_model.54276_t

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

-building trellis in range 1 - 202972
-exon list size: 424


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.6    
2.8    
3.1    
3.3    
3.5    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.2    
5.4    
5.6    
5.9    
6.1    
6.3    
6.6    
6.8    
7.0    
7.3    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.7    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.2    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.5    
53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.3    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 42 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support