-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_7382397-7574635

-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_6812-T1
Valid prediction for snap_scaffold_3-snap.1503-T1
Valid prediction for snap_scaffold_3-snap.1499-T1
Valid prediction for Augustus_model.g4450.t1
Valid prediction for snap_scaffold_3-snap.1522-T1
Valid prediction for snap_scaffold_3-snap.1531-T1
Valid prediction for GlimmerHMM_glimmerT_6820-T1
Valid prediction for snap_scaffold_3-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_6804-T1
Valid prediction for snap_scaffold_3-snap.1515-T1
Valid prediction for GlimmerHMM_glimmerT_6835-T1
Valid prediction for snap_scaffold_3-snap.1527-T1
Valid prediction for GlimmerHMM_glimmerT_6816-T1
Valid prediction for GlimmerHMM_glimmerT_6831-T1
Couldn't classify 38291, 38549
Couldn't classify 38910, 38950
Sorry, prediction pasa_asmbl_40850.p1 fails validation.
(ACG)	 TC	38291-38549	GT	ATG
(TCA)	 AG	38910-38950	AA	GCA
Valid prediction for GlimmerHMM_glimmerT_6818-T1
Valid prediction for GlimmerHMM_glimmerT_6806-T1
Valid prediction for GlimmerHMM_glimmerT_6813-T1
Couldn't classify 39437, 39710
Sorry, prediction pasa_asmbl_40161.p1 fails validation.
(CAG)	 AG	39437-39710	GT	AGG
(TTA)	 AG	39824-39955	GT	CAG
(TTC)	 AG	40059-40163	GT	AGG
(TTC)	 AG	40328-40414	GT	AGG
(AGC)	 AG	40517-40545	GT	GGG
(GAT)	 AG	40636-40677	AG	GAA
-recovered pasa_asmbl_40161.p1, terminal, 40636, 40677
-recovered pasa_asmbl_40161.p1, internal, 39437, 39710
-recovered pasa_asmbl_40161.p1, internal, 39824, 39955
-recovered pasa_asmbl_40161.p1, internal, 40059, 40163
-recovered pasa_asmbl_40161.p1, internal, 40328, 40414
-recovered pasa_asmbl_40161.p1, internal, 40517, 40545
Valid prediction for snap_scaffold_3-snap.1524-T1
Valid prediction for snap_scaffold_3-snap.1508-T1
Valid prediction for Augustus_model.g4438.t1
Valid prediction for snap_scaffold_3-snap.1529-T1
Valid prediction for snap_scaffold_3-snap.1525-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1498-T1
Valid prediction for snap_scaffold_3-snap.1512-T1
Valid prediction for GlimmerHMM_glimmerT_6810-T1
Valid prediction for snap_scaffold_3-snap.1493-T1
Valid prediction for Augustus_model.g4455.t1
Valid prediction for Augustus_model.g4451.t1
Valid prediction for GlimmerHMM_glimmerT_6825-T1
Valid prediction for snap_scaffold_3-snap.1517-T1
Valid prediction for GlimmerHMM_glimmerT_6819-T1
Valid prediction for GlimmerHMM_glimmerT_6829-T1
Valid prediction for GlimmerHMM_glimmerT_6817-T1
Valid prediction for GlimmerHMM_glimmerT_6822-T1
Valid prediction for GlimmerHMM_glimmerT_6834-T1
Valid prediction for CodingQuarry_transcript_46206-T1
Valid prediction for GlimmerHMM_glimmerT_6803-T1
Valid prediction for snap_scaffold_3-snap.1516-T1
Valid prediction for Augustus_model.g4447.t1
Valid prediction for GlimmerHMM_glimmerT_6830-T1
Valid prediction for Augustus_model.g4446.t1
Valid prediction for GlimmerHMM_glimmerT_6828-T1
Valid prediction for snap_scaffold_3-snap.1507-T1
Valid prediction for snap_scaffold_3-snap.1533-T1
Valid prediction for Augustus_model.g4445.t1
Valid prediction for Augustus_model.g4441.t1
Valid prediction for Augustus_model.g4456.t1
Valid prediction for snap_scaffold_3-snap.1520-T1
Valid prediction for snap_scaffold_3-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_6823-T1
Valid prediction for GlimmerHMM_glimmerT_6814-T1
Valid prediction for snap_scaffold_3-snap.1514-T1
Valid prediction for snap_scaffold_3-snap.1530-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_3-snap.1505-T1
Valid prediction for snap_scaffold_3-snap.1494-T1
Valid prediction for GlimmerHMM_glimmerT_6808-T1
Valid prediction for snap_scaffold_3-snap.1536-T1
Valid prediction for snap_scaffold_3-snap.1538-T1
Valid prediction for snap_scaffold_3-snap.1502-T1
Valid prediction for Augustus_model.g4439.t1
Valid prediction for Augustus_model.g4452.t1
Valid prediction for snap_scaffold_3-snap.1518-T1
Valid prediction for snap_scaffold_3-snap.1532-T1
Valid prediction for snap_scaffold_3-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_6811-T1
Valid prediction for Augustus_model.g4443.t1
Couldn't classify 159784, 159886
Sorry, prediction pasa_asmbl_39744.p1 fails validation.
(ATG)	 CC	159315-159425	GT	AGG
(AGT)	 AG	159532-159692	GT	AGG
(GAA)	 AG	159784-159886	GC	AGG
-recovered pasa_asmbl_39744.p1, initial, 159315, 159425
-recovered pasa_asmbl_39744.p1, internal, 159532, 159692
-recovered pasa_asmbl_39744.p1, internal, 159784, 159886
Valid prediction for snap_scaffold_3-snap.1526-T1
Valid prediction for snap_scaffold_3-snap.1510-T1
Valid prediction for snap_scaffold_3-snap.1535-T1
Valid prediction for Augustus_model.g4444.t1
Valid prediction for GlimmerHMM_glimmerT_6815-T1
Valid prediction for GlimmerHMM_glimmerT_6827-T1
Valid prediction for Augustus_model.g4442.t1
Valid prediction for Augustus_model.g4454.t1
Valid prediction for snap_scaffold_3-snap.1495-T1
Valid prediction for snap_scaffold_3-snap.1513-T1
Valid prediction for snap_scaffold_3-snap.1496-T1
Valid prediction for snap_scaffold_3-snap.1534-T1
Valid prediction for Augustus_model.g4440.t1
Valid prediction for Augustus_model.g4448.t1
Valid prediction for GlimmerHMM_glimmerT_6837-T1
Valid prediction for snap_scaffold_3-snap.1528-T1
Valid prediction for snap_scaffold_3-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_6826-T1
Valid prediction for CodingQuarry_transcript_46205-T1
Valid prediction for snap_scaffold_3-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_6833-T1
Valid prediction for GlimmerHMM_glimmerT_6832-T1
Valid prediction for snap_scaffold_3-snap.1519-T1
Valid prediction for GlimmerHMM_glimmerT_6809-T1
Valid prediction for Augustus_model.g4457.t1
Valid prediction for snap_scaffold_3-snap.1509-T1
Valid prediction for snap_scaffold_3-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_6836-T1
Valid prediction for Augustus_model.g4449.t1
Valid prediction for Augustus_model.g4453.t1
Valid prediction for GlimmerHMM_glimmerT_6805-T1
Valid prediction for Augustus_model.g4437.t1
Valid prediction for GlimmerHMM_glimmerT_6824-T1
Valid prediction for GlimmerHMM_glimmerT_6807-T1
Valid prediction for snap_scaffold_3-snap.1497-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1523-T1
Valid prediction for GlimmerHMM_glimmerT_6821-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5391, rend_intergenic: 1976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22019, rend_intergenic: 18332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25718, rend_intergenic: 24207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44274, rend_intergenic: 44187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52622, rend_intergenic: 44294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68756, rend_intergenic: 58480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72502, rend_intergenic: 70270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85629, rend_intergenic: 74044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92106, rend_intergenic: 85670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95698, rend_intergenic: 92217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105132, rend_intergenic: 100130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127752, rend_intergenic: 112212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141589, rend_intergenic: 135452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146771, rend_intergenic: 141960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166688, rend_intergenic: 146773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172839, rend_intergenic: 167574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192239
-exon list size: 406


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 5391, rend_intergenic: 1976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22019, rend_intergenic: 18332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25718, rend_intergenic: 24207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44274, rend_intergenic: 44187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52622, rend_intergenic: 44294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68756, rend_intergenic: 58480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72502, rend_intergenic: 70270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85629, rend_intergenic: 74044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92106, rend_intergenic: 85670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95698, rend_intergenic: 92217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105132, rend_intergenic: 100130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127752, rend_intergenic: 112212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141589, rend_intergenic: 135452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146771, rend_intergenic: 141960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166688, rend_intergenic: 146773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172839, rend_intergenic: 167574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support