-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_3615792-3807449

-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 GeneMark_model.90400_t
Valid prediction for GlimmerHMM_glimmerT_52071-T1
Valid prediction for GlimmerHMM_glimmerT_52054-T1
Valid prediction for GeneMark_model.90407_t
Valid prediction for Augustus_model.g34988.t1
Valid prediction for snap_scaffold_23-snap.725-T1
Valid prediction for HiQ_model.g34989.t1
Valid prediction for pasa_asmbl_30759.p1
Valid prediction for GeneMark_model.90411_t
Valid prediction for snap_scaffold_23-snap.724-T1
Valid prediction for GeneMark_model.90393_t
Valid prediction for snap_scaffold_23-snap.722-T1
Valid prediction for GeneMark_model.90385_t
Valid prediction for GeneMark_model.90384_t
Valid prediction for GeneMark_model.90402_t
Valid prediction for GlimmerHMM_glimmerT_52057-T1
Valid prediction for snap_scaffold_23-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_52066-T1
Valid prediction for GeneMark_model.90408_t
Valid prediction for snap_scaffold_23-snap.723-T1
Couldn't classify 35592, 35852
Couldn't classify 40783, 40867
Sorry, prediction pasa_asmbl_30764.p1 fails validation.
(GCG)	 GC	35592-35852	GT	CGG
(GCT)	 AG	35961-36076	GT	CTG
(AGC)	 AG	37179-37392	GT	AGG
(AAG)	 AG	37640-37716	GT	AGG
(ACA)	 AG	37888-37951	GT	CGG
(TCC)	 AG	39873-40009	GT	AGG
(ATT)	 AG	40131-40202	GT	TGG
(TAT)	 AG	40364-40457	GT	AGG
(AGC)	 AG	40549-40592	GT	AAG
(AGG)	 AG	40783-40867	GG	GCG
-recovered pasa_asmbl_30764.p1, internal, 35961, 36076
-recovered pasa_asmbl_30764.p1, internal, 37179, 37392
-recovered pasa_asmbl_30764.p1, internal, 37640, 37716
-recovered pasa_asmbl_30764.p1, internal, 37888, 37951
-recovered pasa_asmbl_30764.p1, internal, 39873, 40009
-recovered pasa_asmbl_30764.p1, internal, 40131, 40202
-recovered pasa_asmbl_30764.p1, internal, 40364, 40457
-recovered pasa_asmbl_30764.p1, internal, 40549, 40592
Valid prediction for HiQ_model.g34991.t1
Valid prediction for snap_scaffold_23-snap.744-T1
Valid prediction for HiQ_model.g34994.t1
Valid prediction for GeneMark_model.90386_t
Valid prediction for GeneMark_model.90413_t
Valid prediction for snap_scaffold_23-snap.719-T1
Valid prediction for snap_scaffold_23-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_52055-T1
Valid prediction for GeneMark_model.90414_t
Valid prediction for snap_scaffold_23-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_52064-T1
Valid prediction for GeneMark_model.90405_t
Valid prediction for CodingQuarry_transcript_35547-T1
Valid prediction for CodingQuarry_transcript_35548-T1
Valid prediction for GlimmerHMM_glimmerT_52056-T1
Valid prediction for snap_scaffold_23-snap.721-T1
Valid prediction for snap_scaffold_23-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_52059-T1
Valid prediction for snap_scaffold_23-snap.740-T1
Valid prediction for pasa_asmbl_30758.p1
Valid prediction for Augustus_model.g34990.t1
Couldn't classify 30614, 30625
Couldn't classify 34857, 35504
Sorry, prediction pasa_asmbl_30762.p1 fails validation.
(GAC)	 AG	30614-30625	GT	AGG
(GAA)	 AG	31080-31166	GT	AGG
(GAA)	 AG	31404-31440	GT	AAG
(AAC)	 AG	33088-33133	GT	TGG
(TAC)	 AG	34578-34722	GT	AGG
(GCT)	 AG	34857-35504	AC	CGA
-recovered pasa_asmbl_30762.p1, internal, 30614, 30625
-recovered pasa_asmbl_30762.p1, internal, 31080, 31166
-recovered pasa_asmbl_30762.p1, internal, 31404, 31440
-recovered pasa_asmbl_30762.p1, internal, 33088, 33133
-recovered pasa_asmbl_30762.p1, internal, 34578, 34722
Valid prediction for GeneMark_model.90403_t
Valid prediction for GeneMark_model.90391_t
Valid prediction for HiQ_model.g34992.t1
Valid prediction for snap_scaffold_23-snap.732-T1
Valid prediction for snap_scaffold_23-snap.743-T1
Valid prediction for Augustus_model.g35002.t1
Valid prediction for GlimmerHMM_glimmerT_52068-T1
Valid prediction for GeneMark_model.90410_t
Valid prediction for snap_scaffold_23-snap.720-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_23-snap.737-T1
Valid prediction for Augustus_model.g35001.t1
Valid prediction for GeneMark_model.90395_t
Valid prediction for Augustus_model.g34995.t1
Valid prediction for snap_scaffold_23-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_52065-T1
Valid prediction for GeneMark_model.90409_t
Valid prediction for GeneMark_model.90387_t
Valid prediction for GeneMark_model.90394_t
Valid prediction for snap_scaffold_23-snap.729-T1
Valid prediction for snap_scaffold_23-snap.736-T1
Valid prediction for GlimmerHMM_glimmerT_52072-T1
Valid prediction for GeneMark_model.90404_t
Valid prediction for snap_scaffold_23-snap.728-T1
Valid prediction for CodingQuarry_transcript_35549-T1
Valid prediction for snap_scaffold_23-snap.733-T1
Valid prediction for snap_scaffold_23-snap.731-T1
Valid prediction for snap_scaffold_23-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_52067-T1
Valid prediction for snap_scaffold_23-snap.742-T1
Valid prediction for Augustus_model.g34996.t1
Valid prediction for GeneMark_model.90412_t
Valid prediction for GlimmerHMM_glimmerT_52063-T1
Valid prediction for GeneMark_model.90392_t
Valid prediction for snap_scaffold_23-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_52069-T1
Valid prediction for GeneMark_model.90406_t
Valid prediction for GlimmerHMM_glimmerT_52062-T1
Valid prediction for GlimmerHMM_glimmerT_52070-T1
Valid prediction for GeneMark_model.90399_t
Couldn't classify 125497, 125557
Couldn't classify 127121, 127177
Sorry, prediction pasa_asmbl_31535.p1 fails validation.
(TGG)	 GC	125497-125557	GT	AGG
(GTA)	 AG	126111-126222	GT	AGG
(GAG)	 AG	126518-126686	GT	GGG
(AGC)	 AG	127121-127177	CG	AGC
-recovered pasa_asmbl_31535.p1, internal, 126111, 126222
-recovered pasa_asmbl_31535.p1, internal, 126518, 126686
Couldn't classify 86440, 86588
Sorry, prediction pasa_asmbl_31537.p1 fails validation.
(AAA)	 CC	86440-86588	GT	AAG
(CGA)	 AG	89176-89356	GT	AAG
-recovered pasa_asmbl_31537.p1, terminal, 89176, 89356
-recovered pasa_asmbl_31537.p1, internal, 89176, 89356
Valid prediction for snap_scaffold_23-snap.738-T1
Valid prediction for GeneMark_model.90388_t
Valid prediction for Augustus_model.g34997.t1
Couldn't classify 79503, 79648
Sorry, prediction pasa_asmbl_31538.p1 fails validation.
(ATG)	 GT	76006-76288	GT	AGG
(CTC)	 AG	79257-79346	GT	AGG
(CGG)	 AG	79503-79648	AA	GGA
-recovered pasa_asmbl_31538.p1, initial, 76006, 76288
-recovered pasa_asmbl_31538.p1, internal, 79257, 79346
Valid prediction for Augustus_model.g35000.t1
Valid prediction for snap_scaffold_23-snap.730-T1
Valid prediction for GlimmerHMM_glimmerT_52058-T1
Valid prediction for snap_scaffold_23-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_52073-T1
Valid prediction for Augustus_model.g34993.t1
Valid prediction for Augustus_model.g34998.t1
Valid prediction for GlimmerHMM_glimmerT_52061-T1
Valid prediction for GlimmerHMM_glimmerT_52060-T1
Valid prediction for GeneMark_model.90401_t
Valid prediction for GeneMark_model.90398_t
Valid prediction for GeneMark_model.90389_t
Valid prediction for Augustus_model.g34999.t1
Valid prediction for GeneMark_model.90390_t
Valid prediction for GeneMark_model.90396_t
Valid prediction for snap_scaffold_23-snap.745-T1
Valid prediction for GeneMark_model.90397_t
Valid prediction for snap_scaffold_23-snap.739-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41236, rend_intergenic: 37116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151662, rend_intergenic: 151060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191658
-exon list size: 446


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.5    
2.7    
2.9    
3.1    
3.3    
3.6    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.1    
5.4    
5.6    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
10.9    
11.2    
11.4    
11.6    
11.8    
12.1    
12.3    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.6    
17.9    
18.1    
18.3    
18.5    
18.8    
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    
22.5    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.3    
24.6    
24.8    
25.0    
25.2    
25.4    
25.7    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.2    
27.5    
27.7    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.3    
72.5    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.5    
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    
81.2    
81.5    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 41236, rend_intergenic: 37116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151662, rend_intergenic: 151060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support