-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_5436127-5653816

-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 snap_scaffold_8-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_19805-T1
Valid prediction for GlimmerHMM_glimmerT_19784-T1
Valid prediction for Augustus_model.g13148.t1
Valid prediction for Augustus_model.g13151.t1
Valid prediction for Augustus_model.g13161.t1
Valid prediction for GlimmerHMM_glimmerT_19795-T1
Valid prediction for Augustus_model.g13165.t1
Valid prediction for snap_scaffold_8-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_19807-T1
Valid prediction for Augustus_model.g13150.t1
Valid prediction for snap_scaffold_8-snap.1115-T1
Valid prediction for snap_scaffold_8-snap.1114-T1
Valid prediction for snap_scaffold_8-snap.1095-T1
Valid prediction for snap_scaffold_8-snap.1124-T1
Valid prediction for snap_scaffold_8-snap.1087-T1
Valid prediction for Augustus_model.g13168.t1
Valid prediction for snap_scaffold_8-snap.1080-T1
Valid prediction for Augustus_model.g13156.t1
Valid prediction for Augustus_model.g13169.t1
Valid prediction for snap_scaffold_8-snap.1096-T1
Valid prediction for snap_scaffold_8-snap.1110-T1
Valid prediction for snap_scaffold_8-snap.1116-T1
Valid prediction for snap_scaffold_8-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_19806-T1
Valid prediction for GlimmerHMM_glimmerT_19790-T1
Valid prediction for GlimmerHMM_glimmerT_19813-T1
Valid prediction for snap_scaffold_8-snap.1097-T1
Valid prediction for Augustus_model.g13154.t1
Valid prediction for GlimmerHMM_glimmerT_19794-T1
Valid prediction for GlimmerHMM_glimmerT_19798-T1
Valid prediction for snap_scaffold_8-snap.1094-T1
Valid prediction for Augustus_model.g13158.t1
Valid prediction for Augustus_model.g13174.t1
Valid prediction for snap_scaffold_8-snap.1109-T1
Valid prediction for snap_scaffold_8-snap.1082-T1
Valid prediction for snap_scaffold_8-snap.1104-T1
Valid prediction for snap_scaffold_8-snap.1090-T1
Valid prediction for snap_scaffold_8-snap.1084-T1
Valid prediction for Augustus_model.g13164.t1
Valid prediction for GlimmerHMM_glimmerT_19791-T1
Valid prediction for Augustus_model.g13167.t1
Valid prediction for snap_scaffold_8-snap.1089-T1
Valid prediction for Augustus_model.g13155.t1
Valid prediction for snap_scaffold_8-snap.1092-T1
Valid prediction for GlimmerHMM_glimmerT_19793-T1
Valid prediction for snap_scaffold_8-snap.1112-T1
Valid prediction for Augustus_model.g13166.t1
Valid prediction for GlimmerHMM_glimmerT_19808-T1
Valid prediction for Augustus_model.g13159.t1
Valid prediction for snap_scaffold_8-snap.1111-T1
Valid prediction for snap_scaffold_8-snap.1106-T1
Valid prediction for Augustus_model.g13160.t1
Valid prediction for GlimmerHMM_glimmerT_19789-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_8-snap.1108-T1
Valid prediction for snap_scaffold_8-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_19792-T1
Valid prediction for snap_scaffold_8-snap.1093-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_19804-T1
Couldn't classify 32047, 32190
Sorry, prediction pasa_asmbl_51840.p1 fails validation.
(AAA)	 AG	32047-32190	GT	AGG
(GGG)	 AG	32333-32398	GT	GTG
(TCA)	 AG	32520-32585	GT	AAG
(GCA)	 AG	32680-32855	GT	AAG
(TTA)	 AG	32969-33045	GT	AGG
(GCA)	 AG	33228-33361	GT	AGG
(GTC)	 AG	33450-33505	GT	AGG
(GGC)	 AG	33590-33737	GT	AGG
(GCA)	 AG	33844-33935	GT	CAG
(GTA)	 AG	34147-34257	GT	CCG
(GAT)	 AG	34337-34504	GT	AGG
(GTA)	 AG	35080-35220	GT	CAG
(GTA)	 AG	35459-35540	GT	AGG
(TTA)	 AG	35710-35862	AC	GAA
add_exon() Sorry, pasa_asmbl_51840.p1 33450-33505-terminal-2 is invalid.
-recovered pasa_asmbl_51840.p1, terminal, 33450, 33505
add_exon() Sorry, pasa_asmbl_51840.p1 34337-34504-terminal-1 is invalid.
-recovered pasa_asmbl_51840.p1, terminal, 34337, 34504
-recovered pasa_asmbl_51840.p1, terminal, 35710, 35862
-recovered pasa_asmbl_51840.p1, internal, 32047, 32190
-recovered pasa_asmbl_51840.p1, internal, 32333, 32398
-recovered pasa_asmbl_51840.p1, internal, 32520, 32585
-recovered pasa_asmbl_51840.p1, internal, 32680, 32855
-recovered pasa_asmbl_51840.p1, internal, 32969, 33045
-recovered pasa_asmbl_51840.p1, internal, 33228, 33361
-recovered pasa_asmbl_51840.p1, internal, 33450, 33505
-recovered pasa_asmbl_51840.p1, internal, 33590, 33737
-recovered pasa_asmbl_51840.p1, internal, 33844, 33935
-recovered pasa_asmbl_51840.p1, internal, 34147, 34257
-recovered pasa_asmbl_51840.p1, internal, 34337, 34504
-recovered pasa_asmbl_51840.p1, internal, 35080, 35220
-recovered pasa_asmbl_51840.p1, internal, 35459, 35540
Valid prediction for GlimmerHMM_glimmerT_19796-T1
Valid prediction for GlimmerHMM_glimmerT_19810-T1
Valid prediction for snap_scaffold_8-snap.1100-T1
Valid prediction for snap_scaffold_8-snap.1098-T1
Valid prediction for CodingQuarry_transcript_59655-T1
Valid prediction for GlimmerHMM_glimmerT_19799-T1
Valid prediction for pasa_asmbl_51836.p1
Valid prediction for GlimmerHMM_glimmerT_19812-T1
Valid prediction for snap_scaffold_8-snap.1085-T1
Valid prediction for Augustus_model.g13145.t1
Valid prediction for GlimmerHMM_glimmerT_19785-T1
Valid prediction for snap_scaffold_8-snap.1121-T1
Valid prediction for snap_scaffold_8-snap.1120-T1
Valid prediction for Augustus_model.g13171.t1
Valid prediction for snap_scaffold_8-snap.1086-T1
Valid prediction for Augustus_model.g13170.t1
Valid prediction for GlimmerHMM_glimmerT_19801-T1
Valid prediction for GlimmerHMM_glimmerT_19809-T1
Valid prediction for GlimmerHMM_glimmerT_19811-T1
Valid prediction for CodingQuarry_transcript_59656-T1
Valid prediction for snap_scaffold_8-snap.1122-T1
Valid prediction for snap_scaffold_8-snap.1107-T1
Valid prediction for snap_scaffold_8-snap.1117-T1
Valid prediction for Augustus_model.g13152.t1
Valid prediction for Augustus_model.g13146.t1
Valid prediction for Augustus_model.g13149.t1
Valid prediction for GlimmerHMM_glimmerT_19800-T1
Valid prediction for snap_scaffold_8-snap.1102-T1
Valid prediction for CodingQuarry_transcript_59657-T1
Valid prediction for HiQ_model.g13173.t1
Valid prediction for Augustus_model.g13144.t1
Valid prediction for snap_scaffold_8-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_19797-T1
Valid prediction for GlimmerHMM_glimmerT_19788-T1
Valid prediction for Augustus_model.g13157.t1
Valid prediction for Augustus_model.g13163.t1
Valid prediction for snap_scaffold_8-snap.1101-T1
Valid prediction for snap_scaffold_8-snap.1103-T1
Valid prediction for HiQ_model.g13172.t1
Valid prediction for pasa_asmbl_51843.p1
Valid prediction for GlimmerHMM_glimmerT_19803-T1
Valid prediction for Augustus_model.g13175.t1
Valid prediction for snap_scaffold_8-snap.1091-T1
Couldn't classify 31765, 31875
Sorry, prediction pasa_asmbl_51842.p1 fails validation.
(ATG)	 CT	30792-30864	GT	TGG
(ATG)	 AG	31024-31166	GT	TGG
(GTT)	 AG	31256-31382	GT	TGG
(ACC)	 AG	31520-31674	GT	TGG
(TGG)	 AG	31765-31875	AT	ACA
-recovered pasa_asmbl_51842.p1, initial, 30792, 30864
add_exon() Sorry, pasa_asmbl_51842.p1 31024-31166-initial-1 is invalid.
-recovered pasa_asmbl_51842.p1, initial, 31024, 31166
-recovered pasa_asmbl_51842.p1, internal, 31024, 31166
-recovered pasa_asmbl_51842.p1, internal, 31256, 31382
-recovered pasa_asmbl_51842.p1, internal, 31520, 31674
Valid prediction for snap_scaffold_8-snap.1125-T1
Valid prediction for Augustus_model.g13147.t1
Valid prediction for snap_scaffold_8-snap.1081-T1
Valid prediction for GlimmerHMM_glimmerT_19802-T1
Valid prediction for snap_scaffold_8-snap.1119-T1
Valid prediction for snap_scaffold_8-snap.1083-T1
Valid prediction for snap_scaffold_8-snap.1105-T1
Valid prediction for Augustus_model.g13153.t1
Valid prediction for GlimmerHMM_glimmerT_19786-T1
Valid prediction for GlimmerHMM_glimmerT_19787-T1
Valid prediction for HiQ_model.g13162.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16307, rend_intergenic: 16220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17877, rend_intergenic: 16442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25707, rend_intergenic: 19894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33061, rend_intergenic: 25786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56710, rend_intergenic: 52262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70910, rend_intergenic: 57357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76195, rend_intergenic: 75390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105707, rend_intergenic: 102309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217690
-exon list size: 374


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 16307, rend_intergenic: 16220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17877, rend_intergenic: 16442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25707, rend_intergenic: 19894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33061, rend_intergenic: 25786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56710, rend_intergenic: 52262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70910, rend_intergenic: 57357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76195, rend_intergenic: 75390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105707, rend_intergenic: 102309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support