-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_6218217-6317177

-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_55593-T1
Valid prediction for snap_scaffold_25-snap.1314-T1
Valid prediction for snap_scaffold_25-snap.1318-T1
Valid prediction for Augustus_model.g37096.t1
Valid prediction for snap_scaffold_25-snap.1325-T1
Valid prediction for snap_scaffold_25-snap.1311-T1
Valid prediction for CodingQuarry_transcript_38675-T1
Valid prediction for GlimmerHMM_glimmerT_55583-T1
Valid prediction for GeneMark_model.96994_t
Valid prediction for CodingQuarry_transcript_38674-T1
Valid prediction for GlimmerHMM_glimmerT_55600-T1
Valid prediction for snap_scaffold_25-snap.1313-T1
Valid prediction for GlimmerHMM_glimmerT_55586-T1
Valid prediction for pasa_asmbl_34541.p2
Valid prediction for pasa_asmbl_33602.p1
Valid prediction for GlimmerHMM_glimmerT_55592-T1
Valid prediction for GeneMark_model.96981_t
Valid prediction for GeneMark_model.97000_t
Valid prediction for CodingQuarry_transcript_38670-T1
Valid prediction for GlimmerHMM_glimmerT_55589-T1
Valid prediction for GlimmerHMM_glimmerT_55595-T1
Valid prediction for GeneMark_model.96983_t
Valid prediction for GlimmerHMM_glimmerT_55584-T1
Valid prediction for GlimmerHMM_glimmerT_55588-T1
Valid prediction for snap_scaffold_25-snap.1319-T1
Valid prediction for Augustus_model.g37100.t1
Valid prediction for snap_scaffold_25-snap.1323-T1
Valid prediction for snap_scaffold_25-snap.1327-T1
Valid prediction for CodingQuarry_transcript_38673-T1
Valid prediction for GlimmerHMM_glimmerT_55590-T1
Valid prediction for snap_scaffold_25-snap.1316-T1
Valid prediction for snap_scaffold_25-snap.1326-T1
Valid prediction for snap_scaffold_25-snap.1328-T1
Valid prediction for Augustus_model.g37092.t1
Valid prediction for GlimmerHMM_glimmerT_55582-T1
Valid prediction for snap_scaffold_25-snap.1315-T1
Valid prediction for GeneMark_model.96990_t
Valid prediction for HiQ_model.g37095.t1
Valid prediction for GlimmerHMM_glimmerT_55599-T1
Valid prediction for GlimmerHMM_glimmerT_55596-T1
Valid prediction for Augustus_model.g37098.t1
Valid prediction for GeneMark_model.96979_t
Couldn't classify 82963, 82990
Sorry, prediction pasa_asmbl_33607.p1 fails validation.
(TCC)	 AA	82963-82990	GT	CTG
(CCT)	 AG	83113-83224	GT	AGG
(TCT)	 AG	83361-83466	GT	AGG
(GCG)	 AG	83839-83976	GT	AGG
(TTG)	 AG	84119-84232	GT	AGG
(ATG)	 AG	84575-84659	GT	AGG
(GAG)	 AG	84876-85183	AT	AGA
-recovered pasa_asmbl_33607.p1, initial, 84575, 84659
-recovered pasa_asmbl_33607.p1, terminal, 84876, 85183
-recovered pasa_asmbl_33607.p1, internal, 83113, 83224
-recovered pasa_asmbl_33607.p1, internal, 83361, 83466
-recovered pasa_asmbl_33607.p1, internal, 83839, 83976
-recovered pasa_asmbl_33607.p1, internal, 84119, 84232
-recovered pasa_asmbl_33607.p1, internal, 84575, 84659
Valid prediction for GeneMark_model.97001_t
Valid prediction for Augustus_model.g37097.t1
Valid prediction for GeneMark_model.96992_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_55587-T1
Valid prediction for GlimmerHMM_glimmerT_55591-T1
Valid prediction for GeneMark_model.96988_t
Valid prediction for GeneMark_model.96998_t
Valid prediction for GeneMark_model.96980_t
Couldn't classify 24068, 24772
Sorry, prediction pasa_asmbl_34313.p1 fails validation.
(TTG)	 GA	24068-24772	AC	AGA
Valid prediction for snap_scaffold_25-snap.1310-T1
Valid prediction for Augustus_model.g37101.t1
Valid prediction for GlimmerHMM_glimmerT_55601-T1
Valid prediction for GeneMark_model.96987_t
Valid prediction for GeneMark_model.96995_t
Valid prediction for pasa_asmbl_34318.p1
Valid prediction for GeneMark_model.96996_t
Valid prediction for GeneMark_model.96989_t
Valid prediction for GlimmerHMM_glimmerT_55598-T1
Valid prediction for GlimmerHMM_glimmerT_55585-T1
Couldn't classify 24973, 25049
Couldn't classify 25098, 25359
Sorry, prediction CodingQuarry_transcript_38671-T1 fails validation.
(ATG)	 CA	24973-25049	CG	CCC
(TGA)	 AA	25098-25359	CG	AGC
Valid prediction for Augustus_model.g37094.t1
Valid prediction for Augustus_model.g37099.t1
Valid prediction for GeneMark_model.96985_t
Valid prediction for snap_scaffold_25-snap.1317-T1
Valid prediction for snap_scaffold_25-snap.1322-T1
Valid prediction for GeneMark_model.96984_t
Valid prediction for snap_scaffold_25-snap.1329-T1
Valid prediction for snap_scaffold_25-snap.1312-T1
Valid prediction for GeneMark_model.96993_t
Valid prediction for GeneMark_model.96982_t
Valid prediction for snap_scaffold_25-snap.1324-T1
Valid prediction for GlimmerHMM_glimmerT_55597-T1
Valid prediction for snap_scaffold_25-snap.1320-T1
Valid prediction for GeneMark_model.96997_t
Valid prediction for snap_scaffold_25-snap.1321-T1
Valid prediction for Augustus_model.g37093.t1
Valid prediction for GlimmerHMM_glimmerT_55594-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26492, rend_intergenic: 21587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31187, rend_intergenic: 26521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45816, rend_intergenic: 44859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59700, rend_intergenic: 55409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 98961
-exon list size: 279


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.6    
3.9    
4.3    
4.6    
5.0    
5.3    
5.7    
6.0    
6.4    
6.8    
7.1    
7.5    
7.8    
8.2    
8.5    
8.9    
9.3    
9.6    
10.0    
10.3    
10.7    
11.0    
11.4    
11.7    
12.1    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.6    
14.9    
15.3    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.8    
18.1    
18.5    
18.9    
19.2    
19.6    
19.9    
20.3    
20.6    
21.0    
21.4    
21.7    
22.1    
22.4    
22.8    
23.1    
23.5    
23.8    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.7    
27.0    
27.4    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.9    
30.2    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.7    
37.0    
37.4    
37.7    
38.1    
38.4    
38.8    
39.1    
39.5    
39.9    
40.2    
40.6    
40.9    
41.3    
41.6    
42.0    
42.3    
42.7    
43.1    
43.4    
43.8    
44.1    
44.5    
44.8    
45.2    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.7    
48.0    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
52.0    
52.3    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.8    
55.2    
55.5    
55.9    
56.2    
56.6    
56.9    
57.3    
57.7    
58.0    
58.4    
58.7    
59.1    
59.4    
59.8    
60.1    
60.5    
60.9    
61.2    
61.6    
61.9    
62.3    
62.6    
63.0    
63.3    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.8    
70.1    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.6    
73.0    
73.3    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.2    
76.5    
76.9    
77.2    
77.6    
77.9    
78.3    
78.6    
79.0    
79.4    
79.7    
80.1    
80.4    
80.8    
81.1    
81.5    
81.9    
82.2    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.9    
88.3    
88.6    
89.0    
89.3    
89.7    
90.0    
90.4    
90.7    
91.1    
91.5    
91.8    
92.2    
92.5    
92.9    
93.2    
93.6    
94.0    
94.3    
94.7    
95.0    
95.4    
95.7    
96.1    
96.4    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 26492, rend_intergenic: 21587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31187, rend_intergenic: 26521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45816, rend_intergenic: 44859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59700, rend_intergenic: 55409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support