-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_15514709-15751598

-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 GlimmerHMM_glimmerT_10760-T1
Valid prediction for snap_scaffold_4-snap.3149-T1
Valid prediction for snap_scaffold_4-snap.3129-T1
Valid prediction for snap_scaffold_4-snap.3139-T1
Valid prediction for snap_scaffold_4-snap.3143-T1
Valid prediction for Augustus_model.g7060.t1
Valid prediction for snap_scaffold_4-snap.3137-T1
Valid prediction for GlimmerHMM_glimmerT_10743-T1
Valid prediction for GlimmerHMM_glimmerT_10751-T1
Valid prediction for GlimmerHMM_glimmerT_10740-T1
Valid prediction for GlimmerHMM_glimmerT_10746-T1
Valid prediction for snap_scaffold_4-snap.3127-T1
Valid prediction for snap_scaffold_4-snap.3161-T1
Valid prediction for GlimmerHMM_glimmerT_10758-T1
Valid prediction for snap_scaffold_4-snap.3159-T1
Valid prediction for Augustus_model.g7061.t1
Valid prediction for snap_scaffold_4-snap.3135-T1
Valid prediction for snap_scaffold_4-snap.3158-T1
Valid prediction for snap_scaffold_4-snap.3131-T1
Valid prediction for snap_scaffold_4-snap.3153-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g7063.t1
Valid prediction for snap_scaffold_4-snap.3155-T1
Valid prediction for snap_scaffold_4-snap.3124-T1
Valid prediction for snap_scaffold_4-snap.3125-T1
Valid prediction for GlimmerHMM_glimmerT_10745-T1
Valid prediction for Augustus_model.g7057.t1
Valid prediction for snap_scaffold_4-snap.3140-T1
Valid prediction for GlimmerHMM_glimmerT_10741-T1
Valid prediction for GlimmerHMM_glimmerT_10748-T1
Valid prediction for snap_scaffold_4-snap.3126-T1
Valid prediction for snap_scaffold_4-snap.3132-T1
Valid prediction for GlimmerHMM_glimmerT_10755-T1
Valid prediction for snap_scaffold_4-snap.3152-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 pasa_asmbl_43120.p1
Valid prediction for GlimmerHMM_glimmerT_10757-T1
Valid prediction for CodingQuarry_transcript_49260-T1
Valid prediction for Augustus_model.g7065.t1
Valid prediction for snap_scaffold_4-snap.3138-T1
Valid prediction for Augustus_model.g7052.t1
Valid prediction for GlimmerHMM_glimmerT_10735-T1
Valid prediction for GlimmerHMM_glimmerT_10762-T1
Valid prediction for snap_scaffold_4-snap.3154-T1
Valid prediction for snap_scaffold_4-snap.3160-T1
Valid prediction for GlimmerHMM_glimmerT_10742-T1
Valid prediction for snap_scaffold_4-snap.3165-T1
Valid prediction for Augustus_model.g7055.t1
Valid prediction for snap_scaffold_4-snap.3144-T1
Valid prediction for Augustus_model.g7062.t1
Valid prediction for GlimmerHMM_glimmerT_10750-T1
Valid prediction for snap_scaffold_4-snap.3166-T1
Valid prediction for snap_scaffold_4-snap.3157-T1
Valid prediction for GlimmerHMM_glimmerT_10744-T1
Valid prediction for GlimmerHMM_glimmerT_10761-T1
Valid prediction for CodingQuarry_transcript_49259-T1
Valid prediction for GlimmerHMM_glimmerT_10736-T1
Valid prediction for snap_scaffold_4-snap.3162-T1
Valid prediction for Augustus_model.g7056.t1
Valid prediction for Augustus_model.g7050.t1
Valid prediction for GlimmerHMM_glimmerT_10759-T1
Valid prediction for snap_scaffold_4-snap.3147-T1
Valid prediction for snap_scaffold_4-snap.3134-T1
Valid prediction for pasa_asmbl_43101.p1
Valid prediction for snap_scaffold_4-snap.3150-T1
Couldn't classify 95589, 96683
Sorry, prediction pasa_asmbl_43106.p1 fails validation.
(GCC)	 TG	95589-96683	AG	AGA
Couldn't classify 93903, 93995
Couldn't classify 95190, 95534
Sorry, prediction pasa_asmbl_43107.p1 fails validation.
(TTC)	 AG	93903-93995	GT	GGG
(ATC)	 AG	94378-94508	GT	AAG
(GTG)	 AG	94793-94925	GT	AGG
(TGC)	 AG	95190-95534	AG	GCA
-recovered pasa_asmbl_43107.p1, internal, 93903, 93995
-recovered pasa_asmbl_43107.p1, internal, 94378, 94508
-recovered pasa_asmbl_43107.p1, internal, 94793, 94925
Valid prediction for Augustus_model.g7066.t1
Valid prediction for GlimmerHMM_glimmerT_10753-T1
Valid prediction for GlimmerHMM_glimmerT_10766-T1
Valid prediction for Augustus_model.g7053.t1
Valid prediction for snap_scaffold_4-snap.3156-T1
Valid prediction for GlimmerHMM_glimmerT_10764-T1
Valid prediction for snap_scaffold_4-snap.3123-T1
Valid prediction for GlimmerHMM_glimmerT_10765-T1
Couldn't classify 79666, 79708
Couldn't classify 81077, 81169
Sorry, prediction pasa_asmbl_43110.p1 fails validation.
(TTC)	 CT	79666-79708	GT	CGG
(GTG)	 AG	80415-80525	GT	TAG
(GAG)	 AG	80713-80864	GT	GGG
(GAC)	 AG	81077-81169	AA	CAA
-recovered pasa_asmbl_43110.p1, internal, 80415, 80525
-recovered pasa_asmbl_43110.p1, internal, 80713, 80864
Valid prediction for snap_scaffold_4-snap.3148-T1
Valid prediction for snap_scaffold_4-snap.3130-T1
Valid prediction for snap_scaffold_4-snap.3142-T1
Valid prediction for GlimmerHMM_glimmerT_10763-T1
Couldn't classify 88637, 88678
Couldn't classify 89629, 89754
Sorry, prediction pasa_asmbl_43109.p1 fails validation.
(TGG)	 CG	88637-88678	GT	AGG
(AGC)	 AG	88769-88940	GT	TGG
(GGC)	 AG	89158-89321	GT	AGG
(CCC)	 AG	89629-89754	AT	GGA
-recovered pasa_asmbl_43109.p1, internal, 88769, 88940
-recovered pasa_asmbl_43109.p1, internal, 89158, 89321
Couldn't classify 35829, 36051
Sorry, prediction pasa_asmbl_43119.p1 fails validation.
(TCT)	 AC	35829-36051	GT	TGG
(GAA)	 AG	36206-36303	GG	GAG
-recovered pasa_asmbl_43119.p1, terminal, 36206, 36303
Valid prediction for GlimmerHMM_glimmerT_10739-T1
Valid prediction for pasa_asmbl_43111.p1
Valid prediction for CodingQuarry_transcript_49261-T1
Valid prediction for Augustus_model.g7051.t1
Valid prediction for Augustus_model.g7058.t1
Couldn't classify 33965, 34064
Couldn't classify 34814, 34917
Sorry, prediction pasa_asmbl_43611.p1 fails validation.
(GGC)	 TT	33965-34064	GT	CCG
(ATC)	 AG	34333-34608	GT	CTG
(ATG)	 AG	34814-34917	TG	CCT
-recovered pasa_asmbl_43611.p1, internal, 34333, 34608
Valid prediction for snap_scaffold_4-snap.3133-T1
Couldn't classify 58196, 59053
Sorry, prediction pasa_asmbl_43118.p1 fails validation.
(TCC)	 TC	58196-59053	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_10756-T1
Valid prediction for snap_scaffold_4-snap.3146-T1
Valid prediction for GlimmerHMM_glimmerT_10737-T1
Valid prediction for pasa_asmbl_43116.p1
Valid prediction for CodingQuarry_transcript_49262-T1
Valid prediction for Augustus_model.g7059.t1
Valid prediction for GlimmerHMM_glimmerT_10747-T1
Valid prediction for Augustus_model.g7067.t1
Valid prediction for GlimmerHMM_glimmerT_10738-T1
Couldn't classify 92943, 93049
Sorry, prediction pasa_asmbl_43637.p2 fails validation.
(ATG)	 GC	92197-92211	GT	AGG
(TGC)	 AG	92360-92555	GT	TGG
(GTG)	 AG	92943-93049	GA	AGG
-recovered pasa_asmbl_43637.p2, initial, 92197, 92211
-recovered pasa_asmbl_43637.p2, internal, 92360, 92555
Valid prediction for snap_scaffold_4-snap.3151-T1
Valid prediction for Augustus_model.g7064.t1
Valid prediction for snap_scaffold_4-snap.3136-T1
Valid prediction for snap_scaffold_4-snap.3141-T1
Valid prediction for Augustus_model.g7054.t1
Valid prediction for snap_scaffold_4-snap.3145-T1
Couldn't classify 90109, 90299
Couldn't classify 91997, 92007
Sorry, prediction pasa_asmbl_43108.p1 fails validation.
(GCC)	 TG	90109-90299	GT	AGG
(GAC)	 AG	90507-90633	GT	AGG
(CTG)	 AG	91633-91843	GT	GGG
(GTG)	 AG	91997-92007	CG	GGC
-recovered pasa_asmbl_43108.p1, internal, 90507, 90633
-recovered pasa_asmbl_43108.p1, internal, 91633, 91843
Valid prediction for GlimmerHMM_glimmerT_10752-T1
Valid prediction for snap_scaffold_4-snap.3128-T1
Valid prediction for snap_scaffold_4-snap.3164-T1
Valid prediction for GlimmerHMM_glimmerT_10749-T1
Valid prediction for snap_scaffold_4-snap.3163-T1
Valid prediction for GlimmerHMM_glimmerT_10754-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20843, rend_intergenic: 6501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31599, rend_intergenic: 31290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44584, rend_intergenic: 31982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51356, rend_intergenic: 44936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61548, rend_intergenic: 56349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69414, rend_intergenic: 68445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70616, rend_intergenic: 70463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74639, rend_intergenic: 71247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78261, rend_intergenic: 76662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88938, rend_intergenic: 85666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95208, rend_intergenic: 90308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160469, rend_intergenic: 144617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236890
-exon list size: 441


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.0    
2.3    
2.5    
2.7    
2.9    
3.2    
3.4    
3.6    
3.8    
4.1    
4.3    
4.5    
4.7    
5.0    
5.2    
5.4    
5.6    
5.9    
6.1    
6.3    
6.5    
6.8    
7.0    
7.2    
7.4    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
9.9    
10.2    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.7    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.7    
19.0    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.3    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.6    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.5    
34.8    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.0    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.9    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.6    
64.8    
65.0    
65.2    
65.5    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.4    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.0    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 20843, rend_intergenic: 6501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31599, rend_intergenic: 31290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44584, rend_intergenic: 31982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51356, rend_intergenic: 44936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61548, rend_intergenic: 56349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69414, rend_intergenic: 68445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70616, rend_intergenic: 70463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74639, rend_intergenic: 71247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78261, rend_intergenic: 76662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88938, rend_intergenic: 85666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95208, rend_intergenic: 90308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160469, rend_intergenic: 144617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support