-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_2201235-2441736

-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.g7557.t1
Valid prediction for GlimmerHMM_glimmerT_11566-T1
Valid prediction for snap_scaffold_5-snap.450-T1
Valid prediction for snap_scaffold_5-snap.444-T1
Valid prediction for GlimmerHMM_glimmerT_11550-T1
Valid prediction for GlimmerHMM_glimmerT_11571-T1
Valid prediction for Augustus_model.g7566.t1
Valid prediction for snap_scaffold_5-snap.440-T1
Valid prediction for snap_scaffold_5-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_11565-T1
Valid prediction for snap_scaffold_5-snap.447-T1
Valid prediction for Augustus_model.g7553.t1
Valid prediction for snap_scaffold_5-snap.456-T1
Valid prediction for pasa_asmbl_45159.p1
Valid prediction for Augustus_model.g7563.t1
Valid prediction for snap_scaffold_5-snap.463-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.431-T1
Valid prediction for snap_scaffold_5-snap.434-T1
Valid prediction for GlimmerHMM_glimmerT_11568-T1
Valid prediction for snap_scaffold_5-snap.437-T1
Valid prediction for snap_scaffold_5-snap.461-T1
Valid prediction for Augustus_model.g7554.t1
Valid prediction for snap_scaffold_5-snap.443-T1
Valid prediction for GlimmerHMM_glimmerT_11558-T1
Valid prediction for GlimmerHMM_glimmerT_11567-T1
Valid prediction for snap_scaffold_5-snap.433-T1
Valid prediction for snap_scaffold_5-snap.471-T1
Valid prediction for HiQ_model.g7564.t1
Valid prediction for GlimmerHMM_glimmerT_11572-T1
Valid prediction for GlimmerHMM_glimmerT_11569-T1
Valid prediction for snap_scaffold_5-snap.455-T1
Valid prediction for CodingQuarry_transcript_51989-T1
Couldn't classify 11172, 11264
Couldn't classify 14489, 14557
Sorry, prediction pasa_asmbl_45157.p1 fails validation.
(AGC)	 GC	11172-11264	GT	AGG
(GAC)	 AG	11804-11965	GT	AGG
(GAT)	 AG	14489-14557	CT	GAC
-recovered pasa_asmbl_45157.p1, internal, 11804, 11965
Valid prediction for snap_scaffold_5-snap.459-T1
Valid prediction for snap_scaffold_5-snap.460-T1
Valid prediction for snap_scaffold_5-snap.467-T1
Couldn't classify 189223, 189336
Sorry, prediction pasa_asmbl_45161.p1 fails validation.
(ATG)	 AA	187248-187357	GT	AGG
(GAA)	 AG	187822-187942	GT	AGG
(AAC)	 AG	188066-188263	GT	ATG
(GAA)	 AG	188482-188661	GT	GGG
(AGT)	 AG	189223-189336	TC	CCT
-recovered pasa_asmbl_45161.p1, initial, 187248, 187357
-recovered pasa_asmbl_45161.p1, internal, 187822, 187942
-recovered pasa_asmbl_45161.p1, internal, 188066, 188263
-recovered pasa_asmbl_45161.p1, internal, 188482, 188661
Valid prediction for Augustus_model.g7561.t1
Valid prediction for snap_scaffold_5-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_11559-T1
Valid prediction for snap_scaffold_5-snap.457-T1
Couldn't classify 189394, 189602
Sorry, prediction pasa_asmbl_45162.p1 fails validation.
(TCC)	 CC	189394-189602	GT	AGG
(GCT)	 AG	190745-190967	GG	GAG
-recovered pasa_asmbl_45162.p1, terminal, 190745, 190967
Valid prediction for snap_scaffold_5-snap.454-T1
Valid prediction for GlimmerHMM_glimmerT_11573-T1
Valid prediction for GlimmerHMM_glimmerT_11564-T1
Valid prediction for snap_scaffold_5-snap.468-T1
Valid prediction for Augustus_model.g7562.t1
Valid prediction for Augustus_model.g7558.t1
Valid prediction for snap_scaffold_5-snap.449-T1
Valid prediction for GlimmerHMM_glimmerT_11555-T1
Valid prediction for GlimmerHMM_glimmerT_11570-T1
Valid prediction for snap_scaffold_5-snap.435-T1
Couldn't classify 22065, 22127
Couldn't classify 23859, 24029
Sorry, prediction pasa_asmbl_45158.p1 fails validation.
(CTA)	 TC	22065-22127	GT	AGG
(GGT)	 AG	22638-22713	GT	GGG
(GAA)	 AG	23049-23194	GT	AGG
(GTT)	 AG	23859-24029	TG	AGT
-recovered pasa_asmbl_45158.p1, internal, 22638, 22713
-recovered pasa_asmbl_45158.p1, internal, 23049, 23194
Valid prediction for snap_scaffold_5-snap.470-T1
Valid prediction for snap_scaffold_5-snap.469-T1
Valid prediction for Augustus_model.g7548.t1
Valid prediction for Augustus_model.g7565.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_5-snap.451-T1
Valid prediction for Augustus_model.g7555.t1
Valid prediction for GlimmerHMM_glimmerT_11557-T1
Valid prediction for snap_scaffold_5-snap.439-T1
Valid prediction for snap_scaffold_5-snap.472-T1
Valid prediction for snap_scaffold_5-snap.473-T1
Couldn't classify 199195, 199250
Sorry, prediction pasa_asmbl_43885.p1 fails validation.
(ATG)	 CC	198696-199134	GT	AGG
(GGG)	 AG	199195-199250	GC	AGG
-recovered pasa_asmbl_43885.p1, initial, 198696, 199134
-recovered pasa_asmbl_43885.p1, internal, 199195, 199250
Valid prediction for snap_scaffold_5-snap.462-T1
Valid prediction for snap_scaffold_5-snap.442-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.448-T1
Valid prediction for snap_scaffold_5-snap.464-T1
Valid prediction for snap_scaffold_5-snap.438-T1
Valid prediction for Augustus_model.g7560.t1
Valid prediction for snap_scaffold_5-snap.436-T1
Valid prediction for Augustus_model.g7551.t1
Valid prediction for GlimmerHMM_glimmerT_11551-T1
Valid prediction for CodingQuarry_transcript_51992-T1
Valid prediction for Augustus_model.g7559.t1
Valid prediction for snap_scaffold_5-snap.441-T1
Valid prediction for snap_scaffold_5-snap.432-T1
Valid prediction for snap_scaffold_5-snap.458-T1
Valid prediction for GlimmerHMM_glimmerT_11554-T1
Valid prediction for GlimmerHMM_glimmerT_11553-T1
Valid prediction for Augustus_model.g7552.t1
Valid prediction for snap_scaffold_5-snap.474-T1
Valid prediction for pasa_asmbl_43886.p1
Valid prediction for snap_scaffold_5-snap.452-T1
Valid prediction for CodingQuarry_transcript_51990-T1
Valid prediction for Augustus_model.g7549.t1
Valid prediction for CodingQuarry_transcript_51991-T1
Valid prediction for GlimmerHMM_glimmerT_11562-T1
Valid prediction for GlimmerHMM_glimmerT_11556-T1
Valid prediction for Augustus_model.g7550.t1
Valid prediction for snap_scaffold_5-snap.465-T1
Valid prediction for GlimmerHMM_glimmerT_11552-T1
Valid prediction for snap_scaffold_5-snap.446-T1
Valid prediction for GlimmerHMM_glimmerT_11561-T1
Valid prediction for HiQ_model.g7556.t1
Valid prediction for snap_scaffold_5-snap.445-T1
Couldn't classify 206829, 206845
Sorry, prediction pasa_asmbl_43879.p1 fails validation.
(AGT)	 AG	206829-206845	GT	AGG
(GTA)	 AG	206884-207083	GT	TGG
(TCC)	 AG	207559-207671	GC	GAG
-recovered pasa_asmbl_43879.p1, terminal, 207559, 207671
-recovered pasa_asmbl_43879.p1, internal, 206829, 206845
-recovered pasa_asmbl_43879.p1, internal, 206884, 207083
-recovered pasa_asmbl_43879.p1, internal, 207559, 207671
Valid prediction for GlimmerHMM_glimmerT_11560-T1
Valid prediction for GlimmerHMM_glimmerT_11563-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16005, rend_intergenic: 9126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29980, rend_intergenic: 25446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63932, rend_intergenic: 49982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90584, rend_intergenic: 64921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99660, rend_intergenic: 95239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101563, rend_intergenic: 100348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122042, rend_intergenic: 109806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151608, rend_intergenic: 148386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161246, rend_intergenic: 160403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166259, rend_intergenic: 162420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169935, rend_intergenic: 166368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234525, rend_intergenic: 216701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240502
-exon list size: 357


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.1    
3.3    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 16005, rend_intergenic: 9126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29980, rend_intergenic: 25446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63932, rend_intergenic: 49982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90584, rend_intergenic: 64921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99660, rend_intergenic: 95239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101563, rend_intergenic: 100348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122042, rend_intergenic: 109806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151608, rend_intergenic: 148386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161246, rend_intergenic: 160403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166259, rend_intergenic: 162420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169935, rend_intergenic: 166368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234525, rend_intergenic: 216701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support