-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_4195635-4415500

-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_42128-T1
Valid prediction for Augustus_model.g28065.t1
Valid prediction for snap_scaffold_18-snap.871-T1
Valid prediction for Augustus_model.g28067.t1
Couldn't classify 215628, 216124
Sorry, prediction pasa_asmbl_20515.p1 fails validation.
(ATG)	 GA	214968-215088	GT	AGG
(GCA)	 AG	215192-215380	GT	TGG
(GTA)	 AG	215628-216124	AT	GCA
-recovered pasa_asmbl_20515.p1, initial, 214968, 215088
-recovered pasa_asmbl_20515.p1, internal, 215192, 215380
Valid prediction for GlimmerHMM_glimmerT_42133-T1
Valid prediction for snap_scaffold_18-snap.901-T1
Valid prediction for pasa_asmbl_20516.p1
Valid prediction for GlimmerHMM_glimmerT_42130-T1
Valid prediction for snap_scaffold_18-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_42141-T1
Valid prediction for Augustus_model.g28064.t1
Valid prediction for snap_scaffold_18-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_42126-T1
Valid prediction for GlimmerHMM_glimmerT_42139-T1
Couldn't classify 111415, 111473
Couldn't classify 112861, 113160
Sorry, prediction pasa_asmbl_20511.p1 fails validation.
(CAT)	 TC	111415-111473	GT	AAG
(TCT)	 AG	112264-112432	GT	AGG
(GGA)	 AG	112635-112763	GT	AGG
(GAC)	 AG	112861-113160	CC	TCC
-recovered pasa_asmbl_20511.p1, internal, 112264, 112432
-recovered pasa_asmbl_20511.p1, internal, 112635, 112763
Valid prediction for snap_scaffold_18-snap.894-T1
Valid prediction for Augustus_model.g28069.t1
Valid prediction for snap_scaffold_18-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_42124-T1
Valid prediction for snap_scaffold_18-snap.891-T1
Valid prediction for HiQ_model.g28072.t1
Valid prediction for snap_scaffold_18-snap.867-T1
Valid prediction for snap_scaffold_18-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_42140-T1
Valid prediction for snap_scaffold_18-snap.877-T1
Sorry, intron length (5) is less than minimum required (10)
Couldn't classify 106888, 107011
Sorry, prediction pasa_asmbl_20509.p1 fails validation.
(ATG)	 CA	105445-105603	GT	GGG
(GAG)	 AG	105948-105988	GT	AGG
(GCT)	 AG	106888-107011	CG	CCC
-recovered pasa_asmbl_20509.p1, initial, 105445, 105603
-recovered pasa_asmbl_20509.p1, internal, 105948, 105988
Valid prediction for Augustus_model.g28060.t1
Valid prediction for GlimmerHMM_glimmerT_42145-T1
Valid prediction for GlimmerHMM_glimmerT_42132-T1
Valid prediction for GlimmerHMM_glimmerT_42138-T1
Valid prediction for GlimmerHMM_glimmerT_42146-T1
Valid prediction for snap_scaffold_18-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_42147-T1
Valid prediction for Augustus_model.g28068.t1
Valid prediction for CodingQuarry_transcript_23732-T1
Valid prediction for GlimmerHMM_glimmerT_42135-T1
Valid prediction for snap_scaffold_18-snap.875-T1
Valid prediction for snap_scaffold_18-snap.872-T1
Valid prediction for snap_scaffold_18-snap.866-T1
Valid prediction for snap_scaffold_18-snap.880-T1
Valid prediction for snap_scaffold_18-snap.878-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_18-snap.886-T1
Valid prediction for snap_scaffold_18-snap.889-T1
Valid prediction for HiQ_model.g28070.t1
Valid prediction for Augustus_model.g28059.t1
Valid prediction for snap_scaffold_18-snap.899-T1
Valid prediction for Augustus_model.g28063.t1
Valid prediction for snap_scaffold_18-snap.879-T1
Valid prediction for GlimmerHMM_glimmerT_42143-T1
Valid prediction for snap_scaffold_18-snap.869-T1
Valid prediction for snap_scaffold_18-snap.895-T1
Valid prediction for pasa_asmbl_20203.p1
Valid prediction for Augustus_model.g28071.t1
Valid prediction for snap_scaffold_18-snap.865-T1
Valid prediction for snap_scaffold_18-snap.892-T1
Valid prediction for snap_scaffold_18-snap.897-T1
Valid prediction for snap_scaffold_18-snap.887-T1
Valid prediction for GlimmerHMM_glimmerT_42125-T1
Valid prediction for snap_scaffold_18-snap.884-T1
Valid prediction for snap_scaffold_18-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_42136-T1
Valid prediction for GlimmerHMM_glimmerT_42134-T1
Valid prediction for snap_scaffold_18-snap.888-T1
Valid prediction for snap_scaffold_18-snap.873-T1
Valid prediction for snap_scaffold_18-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_42137-T1
Valid prediction for GlimmerHMM_glimmerT_42131-T1
Valid prediction for Augustus_model.g28066.t1
Valid prediction for snap_scaffold_18-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_42127-T1
Valid prediction for snap_scaffold_18-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_42148-T1
Valid prediction for GlimmerHMM_glimmerT_42142-T1
Valid prediction for snap_scaffold_18-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_42129-T1
Valid prediction for snap_scaffold_18-snap.890-T1
Valid prediction for snap_scaffold_18-snap.898-T1
Valid prediction for snap_scaffold_18-snap.883-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 72985, 73198
Couldn't classify 74605, 74744
Sorry, prediction pasa_asmbl_19800.p1 fails validation.
(CTC)	 CC	72985-73198	GT	AGG
(GAG)	 AG	74605-74744	GG	GCG
Valid prediction for Augustus_model.g28061.t1
Valid prediction for Augustus_model.g28062.t1
Valid prediction for CodingQuarry_transcript_23733-T1
Valid prediction for GlimmerHMM_glimmerT_42144-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13267, rend_intergenic: 2926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15974, rend_intergenic: 13317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31506, rend_intergenic: 18169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45747, rend_intergenic: 31659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59795, rend_intergenic: 46090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70519, rend_intergenic: 59815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77851, rend_intergenic: 71065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102831, rend_intergenic: 93706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114738, rend_intergenic: 107964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140540, rend_intergenic: 117427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147783, rend_intergenic: 144932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183285, rend_intergenic: 148663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199586, rend_intergenic: 186993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219866
-exon list size: 385


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 13267, rend_intergenic: 2926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15974, rend_intergenic: 13317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31506, rend_intergenic: 18169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45747, rend_intergenic: 31659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59795, rend_intergenic: 46090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70519, rend_intergenic: 59815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77851, rend_intergenic: 71065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102831, rend_intergenic: 93706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114738, rend_intergenic: 107964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140540, rend_intergenic: 117427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147783, rend_intergenic: 144932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183285, rend_intergenic: 148663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199586, rend_intergenic: 186993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support