-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_11681893-11768951

-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_22-snap.2377-T1
Valid prediction for GlimmerHMM_glimmerT_50298-T1
Valid prediction for GlimmerHMM_glimmerT_50303-T1
Couldn't classify 61006, 61062
Couldn't classify 63933, 64022
Sorry, prediction pasa_asmbl_30424.p1 fails validation.
(CTG)	 AG	61006-61062	GT	TGG
(GCC)	 AG	62337-62443	GT	AGG
(GAA)	 AG	63268-63372	GT	AGG
(GCT)	 AG	63679-63820	GT	AGG
(GAT)	 AG	63933-64022	GG	AAG
-recovered pasa_asmbl_30424.p1, internal, 61006, 61062
-recovered pasa_asmbl_30424.p1, internal, 62337, 62443
-recovered pasa_asmbl_30424.p1, internal, 63268, 63372
-recovered pasa_asmbl_30424.p1, internal, 63679, 63820
Couldn't classify 85555, 86103
Sorry, prediction GlimmerHMM_glimmerT_50305-T1 fails validation.
(ATG)	 TC	80006-80068	GT	TGG
(TTC)	 AG	80161-80324	GT	AGG
(GTC)	 AG	81492-81615	GT	AGG
(GTG)	 AG	81782-81850	GT	AGG
(GTG)	 AG	82103-82277	GT	TGG
(CTT)	 AG	82628-82713	GT	AGG
(ACG)	 AG	82791-82876	GT	GGG
(CGC)	 AG	83836-83913	GT	AAG
(ACT)	 AG	85555-86103	GT	TGG
-recovered GlimmerHMM_glimmerT_50305-T1, initial, 80006, 80068
add_exon() Sorry, GlimmerHMM_glimmerT_50305-T1 80161-80324-terminal-2 is invalid.
-recovered GlimmerHMM_glimmerT_50305-T1, terminal, 80161, 80324
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 80161, 80324
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 81492, 81615
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 81782, 81850
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 82103, 82277
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 82628, 82713
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 82791, 82876
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 83836, 83913
-recovered GlimmerHMM_glimmerT_50305-T1, internal, 85555, 86103
Couldn't classify 22179, 22337
Sorry, prediction pasa_asmbl_30416.p1 fails validation.
(ATG)	 AG	18800-19432	GT	GGG
(TCT)	 AG	22179-22337	GA	GGG
-recovered pasa_asmbl_30416.p1, initial, 18800, 19432
-recovered pasa_asmbl_30416.p1, internal, 18800, 19432
Couldn't classify 33637, 33813
Couldn't classify 34271, 34531
Sorry, prediction pasa_asmbl_30419.p1 fails validation.
(CCC)	 AC	33637-33813	GT	AGG
(GTA)	 AG	34271-34531	AT	GTA
Valid prediction for snap_scaffold_22-snap.2384-T1
Couldn't classify 14553, 14751
Sorry, prediction pasa_asmbl_30412.p1 fails validation.
(ATG)	 GG	11291-11384	GT	CGG
(CTC)	 AG	12535-12713	GT	CAG
(CTG)	 AG	12969-13173	GT	AGG
(GCC)	 AG	13818-13992	GT	GGG
(GGC)	 AG	14553-14751	GG	TGG
-recovered pasa_asmbl_30412.p1, initial, 11291, 11384
-recovered pasa_asmbl_30412.p1, internal, 12535, 12713
-recovered pasa_asmbl_30412.p1, internal, 12969, 13173
-recovered pasa_asmbl_30412.p1, internal, 13818, 13992
Valid prediction for snap_scaffold_22-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_50304-T1
Valid prediction for GlimmerHMM_glimmerT_50302-T1
Valid prediction for snap_scaffold_22-snap.2379-T1
Valid prediction for snap_scaffold_22-snap.2383-T1
Valid prediction for snap_scaffold_22-snap.2373-T1
Valid prediction for snap_scaffold_22-snap.2376-T1
Couldn't classify 48914, 49018
Sorry, prediction pasa_asmbl_30423.p3 fails validation.
(GTG)	 AG	48914-49018	GT	AGG
(GAT)	 AG	49299-49451	GT	AGG
(GAG)	 AG	49878-50014	GT	AAG
(GGA)	 AG	50099-50138	GG	GAG
-recovered pasa_asmbl_30423.p3, terminal, 50099, 50138
-recovered pasa_asmbl_30423.p3, internal, 48914, 49018
-recovered pasa_asmbl_30423.p3, internal, 49299, 49451
-recovered pasa_asmbl_30423.p3, internal, 49878, 50014
Valid prediction for GlimmerHMM_glimmerT_50299-T1
Valid prediction for CodingQuarry_transcript_34316-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_22-snap.2375-T1
Valid prediction for snap_scaffold_22-snap.2378-T1
Valid prediction for snap_scaffold_22-snap.2372-T1
Valid prediction for snap_scaffold_22-snap.2380-T1
Valid prediction for GlimmerHMM_glimmerT_50301-T1
Valid prediction for snap_scaffold_22-snap.2381-T1
Valid prediction for snap_scaffold_22-snap.2382-T1
Valid prediction for GlimmerHMM_glimmerT_50297-T1
Valid prediction for snap_scaffold_22-snap.2374-T1
Valid prediction for snap_scaffold_22-snap.2370-T1
Valid prediction for GlimmerHMM_glimmerT_50300-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12901, rend_intergenic: 11291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16785, rend_intergenic: 12945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19962, rend_intergenic: 17892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22349, rend_intergenic: 20073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28327, rend_intergenic: 25693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36622, rend_intergenic: 33513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42037, rend_intergenic: 36829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77815, rend_intergenic: 52608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82273, rend_intergenic: 78644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 87059
-exon list size: 147


building trellis

0.7    
1.3    
2.0    
2.7    
3.4    
4.0    
4.7    
5.4    
6.0    
6.7    
7.4    
8.1    
8.7    
9.4    
10.1    
10.7    
11.4    
12.1    
12.8    
13.4    
14.1    
14.8    
15.4    
16.1    
16.8    
17.4    
18.1    
18.8    
19.5    
20.1    
20.8    
21.5    
22.1    
22.8    
23.5    
24.2    
24.8    
25.5    
26.2    
26.8    
27.5    
28.2    
28.9    
29.5    
30.2    
30.9    
31.5    
32.2    
32.9    
33.6    
34.2    
34.9    
35.6    
36.2    
36.9    
37.6    
38.3    
38.9    
39.6    
40.3    
40.9    
41.6    
42.3    
43.0    
43.6    
44.3    
45.0    
45.6    
46.3    
47.0    
47.7    
48.3    
49.0    
49.7    
50.3    
51.0    
51.7    
52.3    
53.0    
53.7    
54.4    
55.0    
55.7    
56.4    
57.0    
57.7    
58.4    
59.1    
59.7    
60.4    
61.1    
61.7    
62.4    
63.1    
63.8    
64.4    
65.1    
65.8    
66.4    
67.1    
67.8    
68.5    
69.1    
69.8    
70.5    
71.1    
71.8    
72.5    
73.2    
73.8    
74.5    
75.2    
75.8    
76.5    
77.2    
77.9    
78.5    
79.2    
79.9    
80.5    
81.2    
81.9    
82.6    
83.2    
83.9    
84.6    
85.2    
85.9    
86.6    
87.2    
87.9    
88.6    
89.3    
89.9    
90.6    
91.3    
91.9    
92.6    
93.3    
94.0    
94.6    
95.3    
96.0    
96.6    
97.3    
98.0    
98.7    
99.3    
-found 11 predictions from path traversal
Error with prediction: snap lend_intergenic: 12901, rend_intergenic: 11291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16785, rend_intergenic: 12945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19962, rend_intergenic: 17892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22349, rend_intergenic: 20073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28327, rend_intergenic: 25693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36622, rend_intergenic: 33513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42037, rend_intergenic: 36829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77815, rend_intergenic: 52608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82273, rend_intergenic: 78644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support