-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_4089061-4381079

-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 HiQ_model.g383.t1
Valid prediction for GlimmerHMM_glimmerT_495-T1
Valid prediction for GlimmerHMM_glimmerT_500-T1
Valid prediction for snap_scaffold_1-snap.626-T1
Valid prediction for snap_scaffold_1-snap.594-T1
Couldn't classify 14792, 14842
Sorry, prediction pasa_asmbl_1636.p1 fails validation.
(GGT)	 AG	14792-14842	GT	AGG
(GAG)	 AG	15295-15492	GT	AGG
(GCC)	 AG	16046-16899	GT	CTG
(GAA)	 AG	17199-17448	GT	ATG
(AGA)	 AG	18044-18133	GT	AGG
(CAA)	 AG	18504-18728	GT	ATG
(GTC)	 AG	20442-20612	GT	AGG
(ACC)	 AG	21023-21200	GT	AGG
(AGG)	 AG	21734-21850	GT	AGG
(AAT)	 AG	22152-22418	GT	GAG
(TGG)	 AG	22753-23003	GT	AGG
(GTT)	 AG	23124-23162	CC	AAC
-recovered pasa_asmbl_1636.p1, terminal, 22152, 22418
-recovered pasa_asmbl_1636.p1, terminal, 23124, 23162
-recovered pasa_asmbl_1636.p1, internal, 14792, 14842
-recovered pasa_asmbl_1636.p1, internal, 15295, 15492
-recovered pasa_asmbl_1636.p1, internal, 16046, 16899
-recovered pasa_asmbl_1636.p1, internal, 17199, 17448
-recovered pasa_asmbl_1636.p1, internal, 18044, 18133
-recovered pasa_asmbl_1636.p1, internal, 18504, 18728
-recovered pasa_asmbl_1636.p1, internal, 20442, 20612
-recovered pasa_asmbl_1636.p1, internal, 21023, 21200
-recovered pasa_asmbl_1636.p1, internal, 21734, 21850
-recovered pasa_asmbl_1636.p1, internal, 22152, 22418
-recovered pasa_asmbl_1636.p1, internal, 22753, 23003
Valid prediction for snap_scaffold_1-snap.618-T1
Valid prediction for snap_scaffold_1-snap.592-T1
Valid prediction for snap_scaffold_1-snap.623-T1
Valid prediction for snap_scaffold_1-snap.600-T1
Valid prediction for snap_scaffold_1-snap.613-T1
Valid prediction for snap_scaffold_1-snap.608-T1
Couldn't classify 260398, 260532
Couldn't classify 262689, 262709
Sorry, prediction pasa_asmbl_2793.p1 fails validation.
(GGT)	 CA	260398-260532	GT	AGG
(TGC)	 AG	260669-260789	GT	AGG
(GAA)	 AG	261034-261083	GT	GGG
(GTG)	 AG	262689-262709	AA	GGA
-recovered pasa_asmbl_2793.p1, internal, 260669, 260789
-recovered pasa_asmbl_2793.p1, internal, 261034, 261083
Couldn't classify 29615, 29876
Sorry, prediction pasa_asmbl_1639.p1 fails validation.
(AAA)	 AT	29615-29876	GT	AGG
(GGG)	 AG	30222-30340	GT	AGG
(TTT)	 AG	30951-31079	GT	TGG
(GTG)	 AG	31844-32021	GT	AGG
(TTT)	 AG	32298-32433	GT	TGG
(GAA)	 AG	32643-32746	GT	AGG
(GAG)	 AG	32844-33083	GT	AGG
(GAT)	 AG	33221-33496	GT	AGG
(AGA)	 AG	33932-34092	GT	GAG
(ATT)	 AG	35822-35958	GT	AGG
(ACT)	 AG	36736-36886	GC	AGG
-recovered pasa_asmbl_1639.p1, terminal, 36736, 36886
-recovered pasa_asmbl_1639.p1, internal, 30222, 30340
-recovered pasa_asmbl_1639.p1, internal, 30951, 31079
-recovered pasa_asmbl_1639.p1, internal, 31844, 32021
-recovered pasa_asmbl_1639.p1, internal, 32298, 32433
-recovered pasa_asmbl_1639.p1, internal, 32643, 32746
-recovered pasa_asmbl_1639.p1, internal, 32844, 33083
-recovered pasa_asmbl_1639.p1, internal, 33221, 33496
-recovered pasa_asmbl_1639.p1, internal, 33932, 34092
-recovered pasa_asmbl_1639.p1, internal, 35822, 35958
-recovered pasa_asmbl_1639.p1, internal, 36736, 36886
Valid prediction for GlimmerHMM_glimmerT_482-T1
Valid prediction for snap_scaffold_1-snap.615-T1
Valid prediction for GlimmerHMM_glimmerT_494-T1
Valid prediction for Augustus_model.g391.t1
Valid prediction for HiQ_model.g390.t1
Valid prediction for Augustus_model.g387.t1
Valid prediction for snap_scaffold_1-snap.622-T1
Valid prediction for snap_scaffold_1-snap.588-T1
Valid prediction for GlimmerHMM_glimmerT_487-T1
Valid prediction for snap_scaffold_1-snap.595-T1
Valid prediction for snap_scaffold_1-snap.598-T1
Couldn't classify 5963, 6140
Couldn't classify 7555, 7730
Sorry, prediction pasa_asmbl_1634.p1 fails validation.
(CTG)	 CG	5963-6140	GT	AGG
(ACT)	 AG	7555-7730	CT	ACC
Valid prediction for snap_scaffold_1-snap.609-T1
Valid prediction for snap_scaffold_1-snap.610-T1
Valid prediction for snap_scaffold_1-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_475-T1
Valid prediction for Augustus_model.g393.t1
Valid prediction for snap_scaffold_1-snap.593-T1
Valid prediction for snap_scaffold_1-snap.591-T1
Couldn't classify 211397, 211581
Sorry, prediction pasa_asmbl_1665.p1 fails validation.
(GAG)	 CA	211397-211581	GT	AGG
(AGA)	 AG	213090-213241	GT	AGG
(CCG)	 AG	214978-215094	GT	AGG
(ACC)	 AG	216394-216647	AC	AAA
-recovered pasa_asmbl_1665.p1, terminal, 216394, 216647
-recovered pasa_asmbl_1665.p1, internal, 213090, 213241
-recovered pasa_asmbl_1665.p1, internal, 214978, 215094
Valid prediction for snap_scaffold_1-snap.620-T1
Couldn't classify 14166, 14211
Sorry, prediction pasa_asmbl_1635.p1 fails validation.
(ATG)	 TT	9191-9199	GT	AGG
(GAG)	 AG	9904-9990	GT	AGG
(ATG)	 AG	10395-10511	GT	AGG
(AAA)	 AG	13447-13545	GT	ACG
(GAT)	 AG	13658-13806	GT	AGG
(GGA)	 AG	14166-14211	AG	AGA
-recovered pasa_asmbl_1635.p1, initial, 9191, 9199
-recovered pasa_asmbl_1635.p1, initial, 10395, 10511
-recovered pasa_asmbl_1635.p1, terminal, 13658, 13806
-recovered pasa_asmbl_1635.p1, internal, 9904, 9990
-recovered pasa_asmbl_1635.p1, internal, 10395, 10511
-recovered pasa_asmbl_1635.p1, internal, 13447, 13545
-recovered pasa_asmbl_1635.p1, internal, 13658, 13806
Valid prediction for GlimmerHMM_glimmerT_491-T1
Valid prediction for GlimmerHMM_glimmerT_488-T1
Valid prediction for GlimmerHMM_glimmerT_501-T1
Couldn't classify 5453, 5809
Sorry, prediction pasa_asmbl_1633.p1 fails validation.
(CAA)	 GT	5453-5809	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_473-T1
Couldn't classify 174798, 174841
Couldn't classify 179988, 181060
Sorry, prediction pasa_asmbl_1657.p1 fails validation.
(TCC)	 GC	174798-174841	GT	AGG
(GAC)	 AG	175268-175451	GT	TGG
(CTC)	 AG	175840-175890	GT	AGG
(GTG)	 AG	176094-176216	GT	AGG
(GGG)	 AG	176951-177015	GT	GGG
(GGC)	 AG	177307-177390	GT	AGG
(GTA)	 AG	177640-177752	GT	AGG
(GCT)	 AG	177956-178016	GT	TAG
(TGA)	 AG	178258-178333	GT	TGG
(GTG)	 AG	178726-178855	GT	AGG
(ACG)	 AG	179350-179415	GT	AGG
(GTA)	 AG	179722-179838	GT	AGG
(ACA)	 AG	179988-181060	CC	CCC
-recovered pasa_asmbl_1657.p1, internal, 175268, 175451
-recovered pasa_asmbl_1657.p1, internal, 175840, 175890
-recovered pasa_asmbl_1657.p1, internal, 176094, 176216
-recovered pasa_asmbl_1657.p1, internal, 176951, 177015
-recovered pasa_asmbl_1657.p1, internal, 177307, 177390
-recovered pasa_asmbl_1657.p1, internal, 177640, 177752
-recovered pasa_asmbl_1657.p1, internal, 177956, 178016
-recovered pasa_asmbl_1657.p1, internal, 178258, 178333
-recovered pasa_asmbl_1657.p1, internal, 178726, 178855
-recovered pasa_asmbl_1657.p1, internal, 179350, 179415
-recovered pasa_asmbl_1657.p1, internal, 179722, 179838
Valid prediction for GlimmerHMM_glimmerT_476-T1
Valid prediction for GlimmerHMM_glimmerT_471-T1
Valid prediction for snap_scaffold_1-snap.612-T1
Valid prediction for GlimmerHMM_glimmerT_486-T1
Valid prediction for HiQ_model.g389.t1
Valid prediction for snap_scaffold_1-snap.607-T1
Valid prediction for snap_scaffold_1-snap.597-T1
Valid prediction for snap_scaffold_1-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_485-T1
Valid prediction for Augustus_model.g392.t1
Valid prediction for GlimmerHMM_glimmerT_472-T1
Valid prediction for Augustus_model.g382.t1
Valid prediction for GlimmerHMM_glimmerT_493-T1
Valid prediction for snap_scaffold_1-snap.614-T1
Valid prediction for snap_scaffold_1-snap.604-T1
Valid prediction for snap_scaffold_1-snap.625-T1
Valid prediction for pasa_asmbl_1658.p1
Valid prediction for snap_scaffold_1-snap.606-T1
Valid prediction for pasa_asmbl_1656.p1
Valid prediction for GlimmerHMM_glimmerT_490-T1
Valid prediction for Augustus_model.g385.t1
Valid prediction for snap_scaffold_1-snap.590-T1
Valid prediction for Augustus_model.g380.t1
Valid prediction for pasa_asmbl_1654.p1
Couldn't classify 132536, 133108
Sorry, prediction pasa_asmbl_1640.p1 fails validation.
(CGA)	 CC	132536-133108	GT	AGG
(GTG)	 AG	134562-134644	GT	AAG
(GTT)	 AG	135109-135265	GT	ATG
(GAA)	 AG	135455-135619	GT	AGG
(ATC)	 AG	135942-136067	GT	TGG
(AAA)	 AG	136497-136717	GT	AAG
(GCT)	 AG	137276-137309	AC	GAA
-recovered pasa_asmbl_1640.p1, terminal, 137276, 137309
-recovered pasa_asmbl_1640.p1, internal, 134562, 134644
-recovered pasa_asmbl_1640.p1, internal, 135109, 135265
-recovered pasa_asmbl_1640.p1, internal, 135455, 135619
-recovered pasa_asmbl_1640.p1, internal, 135942, 136067
-recovered pasa_asmbl_1640.p1, internal, 136497, 136717

-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_484-T1
Valid prediction for snap_scaffold_1-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_503-T1
Valid prediction for GlimmerHMM_glimmerT_477-T1
Valid prediction for snap_scaffold_1-snap.599-T1
Valid prediction for CodingQuarry_transcript_2585-T1
Valid prediction for GlimmerHMM_glimmerT_496-T1
Valid prediction for GlimmerHMM_glimmerT_483-T1
Valid prediction for HiQ_model.g386.t1
Valid prediction for GlimmerHMM_glimmerT_478-T1
Valid prediction for HiQ_model.g388.t1
Valid prediction for GlimmerHMM_glimmerT_469-T1
Valid prediction for GlimmerHMM_glimmerT_497-T1
Valid prediction for GlimmerHMM_glimmerT_479-T1
Valid prediction for Augustus_model.g394.t1
Valid prediction for GlimmerHMM_glimmerT_499-T1
Valid prediction for pasa_asmbl_180.p1
Valid prediction for CodingQuarry_transcript_2584-T1
Valid prediction for snap_scaffold_1-snap.602-T1
Valid prediction for GlimmerHMM_glimmerT_481-T1
Valid prediction for snap_scaffold_1-snap.601-T1
Valid prediction for pasa_asmbl_181.p1
Valid prediction for GlimmerHMM_glimmerT_470-T1
Valid prediction for GlimmerHMM_glimmerT_498-T1
Valid prediction for Augustus_model.g384.t1
Valid prediction for GlimmerHMM_glimmerT_492-T1
Valid prediction for snap_scaffold_1-snap.617-T1
Valid prediction for snap_scaffold_1-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_502-T1
Valid prediction for snap_scaffold_1-snap.624-T1
Valid prediction for snap_scaffold_1-snap.611-T1
Valid prediction for snap_scaffold_1-snap.616-T1
Valid prediction for snap_scaffold_1-snap.619-T1
Valid prediction for snap_scaffold_1-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_474-T1
Valid prediction for GlimmerHMM_glimmerT_480-T1
Valid prediction for Augustus_model.g381.t1
Valid prediction for GlimmerHMM_glimmerT_489-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 172537, rend_intergenic: 169879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261710, rend_intergenic: 258419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263642, rend_intergenic: 262015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266782, rend_intergenic: 265448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 292019
-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 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 172537, rend_intergenic: 169879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261710, rend_intergenic: 258419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263642, rend_intergenic: 262015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266782, rend_intergenic: 265448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support