-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_5012164-5220367

-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.g24088.t1
Valid prediction for snap_scaffold_15-snap.1123-T1
Valid prediction for CodingQuarry_transcript_18001-T1
Valid prediction for Augustus_model.g24093.t1
Valid prediction for snap_scaffold_15-snap.1105-T1
Valid prediction for GlimmerHMM_glimmerT_36128-T1
Valid prediction for snap_scaffold_15-snap.1098-T1
Valid prediction for Augustus_model.g24092.t1
Valid prediction for snap_scaffold_15-snap.1094-T1
Valid prediction for Augustus_model.g24099.t1
Valid prediction for snap_scaffold_15-snap.1112-T1
Valid prediction for snap_scaffold_15-snap.1108-T1
Valid prediction for snap_scaffold_15-snap.1093-T1
Valid prediction for snap_scaffold_15-snap.1122-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_36122-T1
Valid prediction for GlimmerHMM_glimmerT_36131-T1
Valid prediction for snap_scaffold_15-snap.1109-T1
Valid prediction for snap_scaffold_15-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_36130-T1
Valid prediction for snap_scaffold_15-snap.1116-T1
Valid prediction for pasa_asmbl_15188.p1
Valid prediction for Augustus_model.g24094.t1
Valid prediction for snap_scaffold_15-snap.1101-T1
Valid prediction for GlimmerHMM_glimmerT_36129-T1
Valid prediction for Augustus_model.g24081.t1
Valid prediction for GlimmerHMM_glimmerT_36136-T1
Valid prediction for snap_scaffold_15-snap.1103-T1
Valid prediction for HiQ_model.g24090.t1
Valid prediction for Augustus_model.g24091.t1
Valid prediction for pasa_asmbl_15191.p1
Valid prediction for snap_scaffold_15-snap.1100-T1
Valid prediction for snap_scaffold_15-snap.1113-T1
Valid prediction for Augustus_model.g24096.t1
Valid prediction for GlimmerHMM_glimmerT_36117-T1
Valid prediction for GlimmerHMM_glimmerT_36141-T1
Valid prediction for snap_scaffold_15-snap.1120-T1
Valid prediction for snap_scaffold_15-snap.1114-T1
Valid prediction for snap_scaffold_15-snap.1124-T1
Valid prediction for snap_scaffold_15-snap.1091-T1
Valid prediction for GlimmerHMM_glimmerT_36138-T1
Valid prediction for GlimmerHMM_glimmerT_36125-T1
Valid prediction for Augustus_model.g24089.t1
Valid prediction for Augustus_model.g24086.t1
Valid prediction for snap_scaffold_15-snap.1117-T1
Valid prediction for Augustus_model.g24097.t1
Valid prediction for GlimmerHMM_glimmerT_36134-T1
Valid prediction for CodingQuarry_transcript_18000-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 GlimmerHMM_glimmerT_36140-T1
Valid prediction for GlimmerHMM_glimmerT_36121-T1
Valid prediction for GlimmerHMM_glimmerT_36135-T1
Valid prediction for snap_scaffold_15-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_36119-T1
Valid prediction for Augustus_model.g24080.t1
Valid prediction for snap_scaffold_15-snap.1092-T1
Valid prediction for snap_scaffold_15-snap.1096-T1
Valid prediction for Augustus_model.g24083.t1
Valid prediction for snap_scaffold_15-snap.1097-T1
Valid prediction for Augustus_model.g24082.t1
Valid prediction for snap_scaffold_15-snap.1115-T1
Valid prediction for snap_scaffold_15-snap.1104-T1
Valid prediction for snap_scaffold_15-snap.1110-T1
Valid prediction for snap_scaffold_15-snap.1106-T1
Valid prediction for Augustus_model.g24084.t1
Valid prediction for GlimmerHMM_glimmerT_36132-T1
Valid prediction for GlimmerHMM_glimmerT_36120-T1
Valid prediction for snap_scaffold_15-snap.1119-T1
Valid prediction for GlimmerHMM_glimmerT_36127-T1
Valid prediction for snap_scaffold_15-snap.1095-T1
Valid prediction for GlimmerHMM_glimmerT_36137-T1
Valid prediction for Augustus_model.g24085.t1
Valid prediction for Augustus_model.g24098.t1
Valid prediction for snap_scaffold_15-snap.1118-T1
Couldn't classify 164001, 164051
Sorry, prediction pasa_asmbl_14191.p1 fails validation.
(GGC)	 CT	164001-164051	GT	AGG
(GTG)	 AG	164360-164578	GT	AGG
(GAC)	 AG	164807-164914	GT	GGG
(GAC)	 AG	165415-165574	GT	TGG
(GAA)	 AG	166050-166168	GT	AGG
(GTG)	 AG	167207-167441	GT	TGG
(GTG)	 AG	167596-167823	GT	TGG
(GTT)	 AG	168096-168367	GT	AGG
(GTG)	 AG	168478-168575	GT	AGG
(AGT)	 AG	168704-168843	GT	AGG
(ATG)	 AG	169117-169124	AT	AAA
-recovered pasa_asmbl_14191.p1, terminal, 169117, 169124
-recovered pasa_asmbl_14191.p1, internal, 164360, 164578
-recovered pasa_asmbl_14191.p1, internal, 164807, 164914
-recovered pasa_asmbl_14191.p1, internal, 165415, 165574
-recovered pasa_asmbl_14191.p1, internal, 166050, 166168
-recovered pasa_asmbl_14191.p1, internal, 167207, 167441
-recovered pasa_asmbl_14191.p1, internal, 167596, 167823
-recovered pasa_asmbl_14191.p1, internal, 168096, 168367
-recovered pasa_asmbl_14191.p1, internal, 168478, 168575
-recovered pasa_asmbl_14191.p1, internal, 168704, 168843
Valid prediction for GlimmerHMM_glimmerT_36118-T1
Valid prediction for GlimmerHMM_glimmerT_36123-T1
Valid prediction for GlimmerHMM_glimmerT_36126-T1
Valid prediction for GlimmerHMM_glimmerT_36139-T1
Valid prediction for GlimmerHMM_glimmerT_36124-T1
Valid prediction for GlimmerHMM_glimmerT_36133-T1
Valid prediction for Augustus_model.g24087.t1
Couldn't classify 37391, 37494
Sorry, prediction pasa_asmbl_14193.p1 fails validation.
(ATG)	 TC	35047-35055	GT	AGG
(CCC)	 AG	35656-35891	GT	CTG
(ACA)	 AG	36070-36151	GT	ATG
(GTG)	 AG	36276-36407	GC	AGG
(GAG)	 AG	36546-36651	GT	AGG
(GTG)	 AG	36742-36799	GT	AGG
(CCT)	 AG	37041-37210	GT	AGG
(ACA)	 AG	37391-37494	AC	CCA
-recovered pasa_asmbl_14193.p1, initial, 35047, 35055
-recovered pasa_asmbl_14193.p1, internal, 35656, 35891
-recovered pasa_asmbl_14193.p1, internal, 36070, 36151
-recovered pasa_asmbl_14193.p1, internal, 36276, 36407
-recovered pasa_asmbl_14193.p1, internal, 36546, 36651
-recovered pasa_asmbl_14193.p1, internal, 36742, 36799
-recovered pasa_asmbl_14193.p1, internal, 37041, 37210
Valid prediction for GlimmerHMM_glimmerT_36116-T1
Valid prediction for snap_scaffold_15-snap.1099-T1
Valid prediction for snap_scaffold_15-snap.1102-T1
Valid prediction for Augustus_model.g24095.t1
Valid prediction for snap_scaffold_15-snap.1121-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56128, rend_intergenic: 54932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85999, rend_intergenic: 83426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103027, rend_intergenic: 101352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123013, rend_intergenic: 118003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159389, rend_intergenic: 146990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164315, rend_intergenic: 160654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183132, rend_intergenic: 179954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204226, rend_intergenic: 183537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 189634, rend_intergenic: 189631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208204
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 56128, rend_intergenic: 54932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85999, rend_intergenic: 83426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103027, rend_intergenic: 101352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123013, rend_intergenic: 118003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159389, rend_intergenic: 146990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164315, rend_intergenic: 160654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183132, rend_intergenic: 179954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204226, rend_intergenic: 183537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 189634, rend_intergenic: 189631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support