-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_2805876-3095644

-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_14-snap.512-T1
Valid prediction for snap_scaffold_14-snap.515-T1
Valid prediction for Augustus_model.g23012.t1
Valid prediction for CodingQuarry_transcript_15553-T1
Valid prediction for GeneMark_model.58534_t
Valid prediction for snap_scaffold_14-snap.493-T1
Couldn't classify 44310, 44369
Sorry, prediction pasa_asmbl_11860.p1 fails validation.
(TTA)	 CT	44310-44369	GT	ACG
(GCA)	 AG	44825-44897	GT	AGG
(GTT)	 AG	45009-45128	GT	AAG
(CAT)	 AG	45233-45298	GT	AGG
(CAA)	 AG	45422-45525	GT	ACG
(GCT)	 AG	45630-45761	GT	AGG
(GGC)	 AG	45857-45973	CA	GAC
-recovered pasa_asmbl_11860.p1, terminal, 44825, 44897
-recovered pasa_asmbl_11860.p1, terminal, 45857, 45973
-recovered pasa_asmbl_11860.p1, internal, 44825, 44897
-recovered pasa_asmbl_11860.p1, internal, 45009, 45128
-recovered pasa_asmbl_11860.p1, internal, 45233, 45298
-recovered pasa_asmbl_11860.p1, internal, 45422, 45525
-recovered pasa_asmbl_11860.p1, internal, 45630, 45761
Valid prediction for GlimmerHMM_glimmerT_34233-T1
Valid prediction for GlimmerHMM_glimmerT_34224-T1
Valid prediction for CodingQuarry_transcript_15551-T1
Valid prediction for pasa_asmbl_11865.p1
Valid prediction for GeneMark_model.58517_t
Valid prediction for HiQ_model.g23029.t1
Valid prediction for GlimmerHMM_glimmerT_34238-T1
Valid prediction for GlimmerHMM_glimmerT_34220-T1
Valid prediction for GlimmerHMM_glimmerT_34235-T1
Valid prediction for snap_scaffold_14-snap.506-T1
Valid prediction for GeneMark_model.58523_t
Valid prediction for snap_scaffold_14-snap.516-T1
Valid prediction for snap_scaffold_14-snap.508-T1
Valid prediction for Augustus_model.g23027.t1
Valid prediction for snap_scaffold_14-snap.513-T1
Valid prediction for Augustus_model.g23015.t1
Valid prediction for GeneMark_model.58529_t
Valid prediction for GeneMark_model.58519_t
Valid prediction for GeneMark_model.58533_t
Valid prediction for HiQ_model.g23021.t1
Valid prediction for snap_scaffold_14-snap.498-T1
Valid prediction for GeneMark_model.58531_t
Valid prediction for snap_scaffold_14-snap.511-T1
Valid prediction for Augustus_model.g23018.t1
Valid prediction for GeneMark_model.58539_t
Valid prediction for snap_scaffold_14-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_34226-T1
Valid prediction for GeneMark_model.58546_t
Valid prediction for GeneMark_model.58542_t
Valid prediction for Augustus_model.g23026.t1
Valid prediction for GeneMark_model.58537_t
Valid prediction for Augustus_model.g23025.t1
Valid prediction for GeneMark_model.58528_t
Valid prediction for Augustus_model.g23023.t1
Valid prediction for GlimmerHMM_glimmerT_34229-T1
Valid prediction for GlimmerHMM_glimmerT_34214-T1
Valid prediction for snap_scaffold_14-snap.521-T1
Couldn't classify 140262, 140431
Sorry, prediction pasa_asmbl_11870.p1 fails validation.
(GAC)	 AG	140262-140431	GT	AGG
(GAC)	 AG	140613-140802	GC	AGG
-recovered pasa_asmbl_11870.p1, terminal, 140613, 140802
-recovered pasa_asmbl_11870.p1, internal, 140262, 140431
-recovered pasa_asmbl_11870.p1, internal, 140613, 140802
Valid prediction for Augustus_model.g23014.t1
Valid prediction for pasa_asmbl_11857.p1
Valid prediction for GeneMark_model.58521_t
Valid prediction for GeneMark_model.58526_t
Valid prediction for GeneMark_model.58525_t
Valid prediction for GlimmerHMM_glimmerT_34222-T1
Valid prediction for GlimmerHMM_glimmerT_34239-T1
Valid prediction for snap_scaffold_14-snap.494-T1
Valid prediction for Augustus_model.g23020.t1
Valid prediction for GlimmerHMM_glimmerT_34218-T1
Valid prediction for GlimmerHMM_glimmerT_34230-T1
Valid prediction for GlimmerHMM_glimmerT_34231-T1
Valid prediction for GlimmerHMM_glimmerT_34219-T1
Valid prediction for GeneMark_model.58540_t
Valid prediction for Augustus_model.g23030.t1
Valid prediction for GeneMark_model.58549_t
Valid prediction for GeneMark_model.58547_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 GlimmerHMM_glimmerT_34225-T1
Valid prediction for GeneMark_model.58548_t
Valid prediction for HiQ_model.g23019.t1
Valid prediction for GeneMark_model.58518_t
Valid prediction for Augustus_model.g23016.t1
Valid prediction for GeneMark_model.58538_t
Valid prediction for snap_scaffold_14-snap.519-T1
Valid prediction for GeneMark_model.58550_t
Valid prediction for GeneMark_model.58543_t
Valid prediction for snap_scaffold_14-snap.522-T1
Valid prediction for Augustus_model.g23017.t1
Valid prediction for snap_scaffold_14-snap.514-T1
Couldn't classify 177825, 177852
Couldn't classify 179945, 180069
Sorry, prediction pasa_asmbl_12969.p1 fails validation.
(AGC)	 AA	177825-177852	GT	CGG
(ATA)	 AG	177991-178169	GC	TGG
(CTG)	 AG	178392-178518	GT	TGG
(ACA)	 AG	178631-178776	GT	AGG
(GAT)	 AG	178961-179134	GT	AGG
(GCA)	 AG	179351-179509	GT	CGG
(GGA)	 AG	179678-179849	GT	AGG
(GCT)	 AG	179945-180069	TC	CCT
-recovered pasa_asmbl_12969.p1, internal, 177991, 178169
-recovered pasa_asmbl_12969.p1, internal, 178392, 178518
-recovered pasa_asmbl_12969.p1, internal, 178631, 178776
-recovered pasa_asmbl_12969.p1, internal, 178961, 179134
-recovered pasa_asmbl_12969.p1, internal, 179351, 179509
-recovered pasa_asmbl_12969.p1, internal, 179678, 179849
Valid prediction for CodingQuarry_transcript_15557-T1
Valid prediction for snap_scaffold_14-snap.495-T1
Valid prediction for CodingQuarry_transcript_15556-T1
Valid prediction for snap_scaffold_14-snap.497-T1
Valid prediction for snap_scaffold_14-snap.504-T1
Valid prediction for Augustus_model.g23022.t1
Valid prediction for GeneMark_model.58524_t
Valid prediction for HiQ_model.g23013.t1
Couldn't classify 177072, 177293
Couldn't classify 177553, 177576
Sorry, prediction pasa_asmbl_12970.p1 fails validation.
(AAG)	 GG	177072-177293	GT	TGG
(GTA)	 AG	177384-177458	GT	AGG
(ATA)	 AG	177553-177576	CT	GCC
-recovered pasa_asmbl_12970.p1, internal, 177384, 177458
Valid prediction for GeneMark_model.58527_t
Valid prediction for snap_scaffold_14-snap.502-T1
Valid prediction for snap_scaffold_14-snap.520-T1
Couldn't classify 181159, 181242
Sorry, prediction pasa_asmbl_12968.p1 fails validation.
(AAC)	 TC	181159-181242	GT	AGG
(GTT)	 AG	181622-181747	GT	AGG
(CTT)	 AG	181863-181982	GT	CAG
(CAA)	 AG	182119-182190	GT	CGG
(CTC)	 AG	182339-182518	CT	GAC
-recovered pasa_asmbl_12968.p1, terminal, 182339, 182518
-recovered pasa_asmbl_12968.p1, internal, 181622, 181747
-recovered pasa_asmbl_12968.p1, internal, 181863, 181982
-recovered pasa_asmbl_12968.p1, internal, 182119, 182190
Valid prediction for snap_scaffold_14-snap.500-T1
Valid prediction for GeneMark_model.58520_t
Valid prediction for snap_scaffold_14-snap.517-T1
Valid prediction for GlimmerHMM_glimmerT_34228-T1
Valid prediction for GlimmerHMM_glimmerT_34232-T1
Valid prediction for GeneMark_model.58532_t
Valid prediction for snap_scaffold_14-snap.518-T1
Valid prediction for GlimmerHMM_glimmerT_34216-T1
Valid prediction for GlimmerHMM_glimmerT_34236-T1
Valid prediction for CodingQuarry_transcript_15554-T1
Valid prediction for snap_scaffold_14-snap.507-T1
Valid prediction for Augustus_model.g23033.t1
Valid prediction for snap_scaffold_14-snap.505-T1
Valid prediction for snap_scaffold_14-snap.509-T1
Valid prediction for snap_scaffold_14-snap.524-T1
Valid prediction for GlimmerHMM_glimmerT_34240-T1
Valid prediction for Augustus_model.g23024.t1
Valid prediction for GlimmerHMM_glimmerT_34223-T1
Valid prediction for snap_scaffold_14-snap.496-T1
Couldn't classify 152536, 152641
Sorry, prediction pasa_asmbl_12974.p1 fails validation.
(CAG)	 CA	152536-152641	GT	AGG
(CGT)	 AG	153067-153193	GT	GGG
(GTT)	 AG	153609-153708	GT	CAG
(ATG)	 AG	154113-154268	GT	TGG
(GCA)	 AG	154713-154805	TA	AAT
-recovered pasa_asmbl_12974.p1, initial, 154113, 154268
-recovered pasa_asmbl_12974.p1, terminal, 154713, 154805
-recovered pasa_asmbl_12974.p1, internal, 153067, 153193
-recovered pasa_asmbl_12974.p1, internal, 153609, 153708
-recovered pasa_asmbl_12974.p1, internal, 154113, 154268
Valid prediction for GeneMark_model.58545_t
Valid prediction for snap_scaffold_14-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_34215-T1
Valid prediction for GeneMark_model.58530_t
Valid prediction for CodingQuarry_transcript_15552-T1
Valid prediction for HiQ_model.g23028.t1
Valid prediction for GlimmerHMM_glimmerT_34241-T1
Valid prediction for Augustus_model.g23031.t1
Valid prediction for GlimmerHMM_glimmerT_34221-T1
Valid prediction for GlimmerHMM_glimmerT_34217-T1
Valid prediction for snap_scaffold_14-snap.523-T1
Couldn't classify 190376, 190388
Couldn't classify 191529, 191548
Sorry, prediction pasa_asmbl_12967.p1 fails validation.
(GAA)	 CG	190376-190388	GT	CGG
(CAT)	 AG	190747-190924	GT	AGG
(AAT)	 AG	191043-191188	GT	AGG
(CTA)	 AG	191269-191442	GT	AAG
(GTA)	 AG	191529-191548	AA	GCA
-recovered pasa_asmbl_12967.p1, internal, 190747, 190924
-recovered pasa_asmbl_12967.p1, internal, 191043, 191188
-recovered pasa_asmbl_12967.p1, internal, 191269, 191442
Valid prediction for GeneMark_model.58541_t
Couldn't classify 205425, 205617
Sorry, prediction pasa_asmbl_12963.p1 fails validation.
(ATA)	 AA	205425-205617	GT	AGG
(ACA)	 AG	205761-205857	GT	AAG
(GTA)	 AG	206019-206116	GT	TGG
(TTA)	 AG	206249-206427	GT	AGG
(GAT)	 AG	206536-206669	GT	AGG
(GAA)	 AG	206747-206863	GT	AAG
(ACT)	 AG	206992-207116	GT	AGG
(CTG)	 AG	207827-207891	GT	AGG
(AAC)	 AG	208848-208964	AG	GAA
-recovered pasa_asmbl_12963.p1, terminal, 208848, 208964
-recovered pasa_asmbl_12963.p1, internal, 205761, 205857
-recovered pasa_asmbl_12963.p1, internal, 206019, 206116
-recovered pasa_asmbl_12963.p1, internal, 206249, 206427
-recovered pasa_asmbl_12963.p1, internal, 206536, 206669
-recovered pasa_asmbl_12963.p1, internal, 206747, 206863
-recovered pasa_asmbl_12963.p1, internal, 206992, 207116
-recovered pasa_asmbl_12963.p1, internal, 207827, 207891
Valid prediction for snap_scaffold_14-snap.525-T1
Valid prediction for GlimmerHMM_glimmerT_34237-T1
Couldn't classify 175584, 175649
Couldn't classify 177063, 177071
Sorry, prediction pasa_asmbl_12971.p1 fails validation.
(AAA)	 GG	175584-175649	GT	GGG
(ATG)	 AG	175841-175983	GT	AGG
(GGG)	 AG	176124-176223	GT	AAG
(GTC)	 AG	176304-176465	GT	TGG
(ATC)	 AG	176735-176887	GT	CTG
(TTT)	 AG	177063-177071	AA	GGA
-recovered pasa_asmbl_12971.p1, initial, 175841, 175983
-recovered pasa_asmbl_12971.p1, internal, 175841, 175983
-recovered pasa_asmbl_12971.p1, internal, 176124, 176223
-recovered pasa_asmbl_12971.p1, internal, 176304, 176465
-recovered pasa_asmbl_12971.p1, internal, 176735, 176887
Valid prediction for GeneMark_model.58536_t
Valid prediction for GeneMark_model.58522_t
Couldn't classify 191986, 192038
Sorry, prediction pasa_asmbl_12966.p1 fails validation.
(GCC)	 CC	191986-192038	GT	CCG
(GTC)	 AG	192756-192928	GT	GAG
(AGG)	 AG	193310-193431	AA	AAA
-recovered pasa_asmbl_12966.p1, terminal, 193310, 193431
-recovered pasa_asmbl_12966.p1, internal, 192756, 192928
Valid prediction for snap_scaffold_14-snap.501-T1
Valid prediction for Augustus_model.g23032.t1
Valid prediction for snap_scaffold_14-snap.503-T1
Couldn't classify 270011, 270084
Couldn't classify 279185, 279325
Sorry, prediction pasa_asmbl_12959.p1 fails validation.
(TTC)	 CC	270011-270084	GT	ACG
(GTA)	 AG	270360-270462	GT	TGG
(GGG)	 AG	270968-271147	GT	AGG
(GAG)	 AG	271657-271821	GT	AGG
(CTC)	 AG	272070-272230	GT	AGG
(GTA)	 AG	273001-273076	GT	GGG
(GAG)	 AG	274025-274173	GT	CAG
(GAG)	 AG	274347-274443	GT	AGG
(GTT)	 AG	274579-274683	GT	AGG
(GGA)	 AG	275064-275159	GT	AGG
(TAT)	 AG	275303-275437	GT	TGG
(GTT)	 AG	275654-275770	GT	AGG
(GCA)	 AG	275926-276105	GT	AGG
(AAA)	 AG	276374-276571	GT	AGG
(GAC)	 AG	276983-277123	GT	ATG
(GGC)	 AG	277388-277459	GT	AGG
(GTG)	 AG	279185-279325	GT	AGG
-recovered pasa_asmbl_12959.p1, internal, 270360, 270462
-recovered pasa_asmbl_12959.p1, internal, 270968, 271147
-recovered pasa_asmbl_12959.p1, internal, 271657, 271821
-recovered pasa_asmbl_12959.p1, internal, 272070, 272230
-recovered pasa_asmbl_12959.p1, internal, 273001, 273076
-recovered pasa_asmbl_12959.p1, internal, 274025, 274173
-recovered pasa_asmbl_12959.p1, internal, 274347, 274443
-recovered pasa_asmbl_12959.p1, internal, 274579, 274683
-recovered pasa_asmbl_12959.p1, internal, 275064, 275159
-recovered pasa_asmbl_12959.p1, internal, 275303, 275437
-recovered pasa_asmbl_12959.p1, internal, 275654, 275770
-recovered pasa_asmbl_12959.p1, internal, 275926, 276105
-recovered pasa_asmbl_12959.p1, internal, 276374, 276571
-recovered pasa_asmbl_12959.p1, internal, 276983, 277123
-recovered pasa_asmbl_12959.p1, internal, 277388, 277459
-recovered pasa_asmbl_12959.p1, internal, 279185, 279325
Valid prediction for GlimmerHMM_glimmerT_34227-T1
Valid prediction for GlimmerHMM_glimmerT_34234-T1
Valid prediction for GeneMark_model.58544_t

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

-building trellis in range 1 - 289769
-exon list size: 453


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.2    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.5    
12.7    
13.0    
13.2    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.2    
18.5    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.2    
26.4    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.0    
49.2    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.8    
51.0    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 26 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support