-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_7713317-7937107

-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 Augustus_model.g6290.t1
Valid prediction for snap_scaffold_4-snap.1642-T1
Couldn't classify 100976, 101473
Sorry, prediction pasa_asmbl_41521.p1 fails validation.
(CCA)	 GA	100976-101473	TG	GAT
Valid prediction for snap_scaffold_4-snap.1646-T1
Couldn't classify 66262, 66369
Sorry, prediction pasa_asmbl_41519.p1 fails validation.
(GAA)	 AG	66262-66369	GT	AGG
(ACA)	 AG	66651-66853	GT	AGG
(TTC)	 AG	67194-67378	GT	TGG
(GTA)	 AG	67744-67902	GT	GGG
(GTC)	 AG	68066-68160	GT	AGG
(GAG)	 AG	68639-68797	GT	AGG
(ATG)	 AG	68990-69349	TG	GAT
-recovered pasa_asmbl_41519.p1, terminal, 68990, 69349
-recovered pasa_asmbl_41519.p1, internal, 66262, 66369
-recovered pasa_asmbl_41519.p1, internal, 66651, 66853
-recovered pasa_asmbl_41519.p1, internal, 67194, 67378
-recovered pasa_asmbl_41519.p1, internal, 67744, 67902
-recovered pasa_asmbl_41519.p1, internal, 68066, 68160
-recovered pasa_asmbl_41519.p1, internal, 68639, 68797
Valid prediction for GlimmerHMM_glimmerT_9709-T1
Valid prediction for snap_scaffold_4-snap.1653-T1
Valid prediction for snap_scaffold_4-snap.1676-T1
Valid prediction for snap_scaffold_4-snap.1666-T1
Valid prediction for Augustus_model.g6293.t1
Valid prediction for snap_scaffold_4-snap.1655-T1
Valid prediction for snap_scaffold_4-snap.1671-T1
Valid prediction for snap_scaffold_4-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_9715-T1
Valid prediction for pasa_asmbl_41515.p1
Valid prediction for HiQ_model.g6289.t1
Valid prediction for GlimmerHMM_glimmerT_9706-T1
Valid prediction for GlimmerHMM_glimmerT_9695-T1
Valid prediction for GlimmerHMM_glimmerT_9696-T1
Valid prediction for Augustus_model.g6298.t1
Valid prediction for snap_scaffold_4-snap.1647-T1
Valid prediction for snap_scaffold_4-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_9691-T1
Valid prediction for snap_scaffold_4-snap.1662-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g6304.t1
Valid prediction for snap_scaffold_4-snap.1643-T1
Couldn't classify 43866, 43952
Sorry, prediction pasa_asmbl_41517.p1 fails validation.
(CTG)	 CC	43866-43952	GT	AGG
(GTG)	 AG	44136-44287	GT	AGG
(GCA)	 AG	44450-44582	GT	ACG
(GTG)	 AG	44760-44880	GT	AGG
(GTT)	 AG	45100-45281	AG	GAA
-recovered pasa_asmbl_41517.p1, terminal, 45100, 45281
-recovered pasa_asmbl_41517.p1, internal, 44136, 44287
-recovered pasa_asmbl_41517.p1, internal, 44450, 44582
-recovered pasa_asmbl_41517.p1, internal, 44760, 44880
Valid prediction for Augustus_model.g6295.t1
Valid prediction for Augustus_model.g6297.t1
Valid prediction for snap_scaffold_4-snap.1652-T1
Valid prediction for Augustus_model.g6291.t1
Valid prediction for snap_scaffold_4-snap.1639-T1
Valid prediction for Augustus_model.g6296.t1
Valid prediction for CodingQuarry_transcript_49063-T1
Valid prediction for snap_scaffold_4-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_9693-T1
Valid prediction for snap_scaffold_4-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_9689-T1
Valid prediction for snap_scaffold_4-snap.1651-T1
Valid prediction for GlimmerHMM_glimmerT_9694-T1
Valid prediction for GlimmerHMM_glimmerT_9699-T1
Valid prediction for snap_scaffold_4-snap.1641-T1
Valid prediction for GlimmerHMM_glimmerT_9697-T1
Valid prediction for Augustus_model.g6292.t1
Valid prediction for snap_scaffold_4-snap.1678-T1
Valid prediction for snap_scaffold_4-snap.1670-T1
Valid prediction for GlimmerHMM_glimmerT_9688-T1
Valid prediction for snap_scaffold_4-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_9713-T1
Valid prediction for GlimmerHMM_glimmerT_9692-T1
Valid prediction for GlimmerHMM_glimmerT_9700-T1
Valid prediction for snap_scaffold_4-snap.1681-T1
Valid prediction for snap_scaffold_4-snap.1650-T1
Valid prediction for Augustus_model.g6294.t1
Valid prediction for snap_scaffold_4-snap.1640-T1
Valid prediction for Augustus_model.g6301.t1
Valid prediction for Augustus_model.g6288.t1
Valid prediction for snap_scaffold_4-snap.1645-T1
Valid prediction for snap_scaffold_4-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_9701-T1
Valid prediction for snap_scaffold_4-snap.1667-T1
Valid prediction for snap_scaffold_4-snap.1682-T1
Valid prediction for Augustus_model.g6287.t1
Valid prediction for snap_scaffold_4-snap.1648-T1
Valid prediction for snap_scaffold_4-snap.1679-T1
Valid prediction for GlimmerHMM_glimmerT_9690-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_4-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_9711-T1
Valid prediction for Augustus_model.g6300.t1
Valid prediction for GlimmerHMM_glimmerT_9710-T1
Valid prediction for GlimmerHMM_glimmerT_9707-T1
Valid prediction for GlimmerHMM_glimmerT_9698-T1
Valid prediction for snap_scaffold_4-snap.1668-T1
Valid prediction for GlimmerHMM_glimmerT_9712-T1
Valid prediction for snap_scaffold_4-snap.1637-T1
Valid prediction for snap_scaffold_4-snap.1683-T1
Valid prediction for snap_scaffold_4-snap.1659-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9708-T1
Valid prediction for snap_scaffold_4-snap.1644-T1
Valid prediction for Augustus_model.g6286.t1
Valid prediction for snap_scaffold_4-snap.1677-T1
Valid prediction for GlimmerHMM_glimmerT_9702-T1
Valid prediction for snap_scaffold_4-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_9704-T1
Valid prediction for Augustus_model.g6299.t1
Valid prediction for GlimmerHMM_glimmerT_9714-T1
Valid prediction for snap_scaffold_4-snap.1673-T1
Valid prediction for snap_scaffold_4-snap.1657-T1
Valid prediction for snap_scaffold_4-snap.1672-T1
Valid prediction for Augustus_model.g6303.t1
Valid prediction for Augustus_model.g6302.t1
Valid prediction for GlimmerHMM_glimmerT_9705-T1
Valid prediction for snap_scaffold_4-snap.1684-T1
Valid prediction for snap_scaffold_4-snap.1661-T1
Valid prediction for snap_scaffold_4-snap.1663-T1
Valid prediction for GlimmerHMM_glimmerT_9703-T1
Valid prediction for snap_scaffold_4-snap.1680-T1
Valid prediction for snap_scaffold_4-snap.1638-T1
Valid prediction for snap_scaffold_4-snap.1649-T1
Valid prediction for GlimmerHMM_glimmerT_9687-T1
Valid prediction for snap_scaffold_4-snap.1658-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 148341, rend_intergenic: 148338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124984, rend_intergenic: 120711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131858, rend_intergenic: 126454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134939, rend_intergenic: 133183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137374, rend_intergenic: 136182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150627, rend_intergenic: 138422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162881, rend_intergenic: 151738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166646, rend_intergenic: 162941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175542, rend_intergenic: 168717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182682, rend_intergenic: 178427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192241, rend_intergenic: 188542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206266, rend_intergenic: 193362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223791
-exon list size: 434


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 148341, rend_intergenic: 148338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124984, rend_intergenic: 120711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131858, rend_intergenic: 126454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134939, rend_intergenic: 133183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137374, rend_intergenic: 136182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150627, rend_intergenic: 138422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162881, rend_intergenic: 151738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166646, rend_intergenic: 162941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175542, rend_intergenic: 168717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182682, rend_intergenic: 178427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192241, rend_intergenic: 188542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206266, rend_intergenic: 193362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support