-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_944880-1135938

-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_1-snap.186-T1
Valid prediction for Augustus_model.g116.t1
Valid prediction for GlimmerHMM_glimmerT_124-T1
Valid prediction for Augustus_model.g110.t1
Valid prediction for GlimmerHMM_glimmerT_136-T1
Valid prediction for GlimmerHMM_glimmerT_143-T1
Valid prediction for snap_scaffold_1-snap.202-T1
Valid prediction for Augustus_model.g113.t1
Valid prediction for GlimmerHMM_glimmerT_127-T1
Couldn't classify 94856, 95079
Sorry, prediction pasa_asmbl_1454.p2 fails validation.
(GAT)	 GG	94856-95079	GT	TGG
(GTA)	 AG	96602-96905	TC	GAT
-recovered pasa_asmbl_1454.p2, terminal, 96602, 96905
Valid prediction for GlimmerHMM_glimmerT_129-T1
Valid prediction for snap_scaffold_1-snap.174-T1
Valid prediction for snap_scaffold_1-snap.188-T1
Valid prediction for Augustus_model.g115.t1
Valid prediction for CodingQuarry_transcript_2517-T1
Valid prediction for GlimmerHMM_glimmerT_146-T1
Valid prediction for snap_scaffold_1-snap.201-T1
Couldn't classify 43463, 43579
Sorry, prediction pasa_asmbl_1448.p1 fails validation.
(CTC)	 CT	43463-43579	GT	AGG
(CTG)	 AG	43949-44022	GT	GTG
(CTA)	 AG	44167-44260	GT	CTG
(GTG)	 AG	45765-45832	GT	ATG
(GAA)	 AG	46145-46215	GT	TGG
(ACA)	 AG	46367-46416	TT	GAT
-recovered pasa_asmbl_1448.p1, terminal, 46367, 46416
-recovered pasa_asmbl_1448.p1, internal, 43949, 44022
-recovered pasa_asmbl_1448.p1, internal, 44167, 44260
-recovered pasa_asmbl_1448.p1, internal, 45765, 45832
-recovered pasa_asmbl_1448.p1, internal, 46145, 46215
Valid prediction for snap_scaffold_1-snap.206-T1
Valid prediction for CodingQuarry_transcript_2512-T1
Valid prediction for snap_scaffold_1-snap.179-T1
Valid prediction for GlimmerHMM_glimmerT_138-T1
Valid prediction for GlimmerHMM_glimmerT_132-T1
Valid prediction for GlimmerHMM_glimmerT_144-T1
Valid prediction for Augustus_model.g107.t1
Valid prediction for GlimmerHMM_glimmerT_122-T1
Valid prediction for snap_scaffold_1-snap.196-T1
Valid prediction for snap_scaffold_1-snap.175-T1
Valid prediction for snap_scaffold_1-snap.197-T1
Valid prediction for snap_scaffold_1-snap.195-T1
Valid prediction for snap_scaffold_1-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_141-T1
Couldn't classify 103096, 103180
Sorry, prediction pasa_asmbl_1456.p1 fails validation.
(GAA)	 AA	103096-103180	GT	AGG
(ATG)	 AG	105913-106850	AA	AAA
-recovered pasa_asmbl_1456.p1, terminal, 105913, 106850
Valid prediction for snap_scaffold_1-snap.177-T1
Valid prediction for snap_scaffold_1-snap.199-T1
Valid prediction for snap_scaffold_1-snap.191-T1
Valid prediction for snap_scaffold_1-snap.198-T1
Valid prediction for pasa_asmbl_1445.p1
Valid prediction for HiQ_model.g102.t1
Valid prediction for snap_scaffold_1-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_145-T1
Valid prediction for snap_scaffold_1-snap.182-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 CodingQuarry_transcript_2513-T1
Valid prediction for snap_scaffold_1-snap.204-T1
Valid prediction for snap_scaffold_1-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_150-T1
Valid prediction for GlimmerHMM_glimmerT_133-T1
Valid prediction for snap_scaffold_1-snap.193-T1
Valid prediction for pasa_asmbl_45.p1
Valid prediction for GlimmerHMM_glimmerT_139-T1
Valid prediction for snap_scaffold_1-snap.205-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_123-T1
Valid prediction for GlimmerHMM_glimmerT_121-T1
Valid prediction for Augustus_model.g111.t1
Valid prediction for CodingQuarry_transcript_2514-T1
Valid prediction for CodingQuarry_transcript_2515-T1
Couldn't classify 99962, 100474
Sorry, prediction pasa_asmbl_1451.p1 fails validation.
(CAC)	 CT	99962-100474	GA	AGG
Valid prediction for snap_scaffold_1-snap.192-T1
Valid prediction for Augustus_model.g112.t1
Valid prediction for Augustus_model.g105.t1
Valid prediction for Augustus_model.g109.t1
Valid prediction for snap_scaffold_1-snap.184-T1
Valid prediction for snap_scaffold_1-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_149-T1
Valid prediction for GlimmerHMM_glimmerT_128-T1
Valid prediction for Augustus_model.g114.t1
Valid prediction for GlimmerHMM_glimmerT_148-T1
Valid prediction for Augustus_model.g101.t1
Valid prediction for Augustus_model.g103.t1
Valid prediction for Augustus_model.g117.t1
Valid prediction for snap_scaffold_1-snap.180-T1
Valid prediction for GlimmerHMM_glimmerT_135-T1
Valid prediction for snap_scaffold_1-snap.178-T1
Couldn't classify 156381, 156499
Sorry, prediction pasa_asmbl_43.p1 fails validation.
(CAG)	 AG	156381-156499	GT	TGG
(GAG)	 AG	156880-157015	GT	GGG
(GGA)	 AG	157356-157479	GT	GGG
(TGT)	 AG	157966-158048	GG	GAG
-recovered pasa_asmbl_43.p1, terminal, 157966, 158048
-recovered pasa_asmbl_43.p1, internal, 156381, 156499
-recovered pasa_asmbl_43.p1, internal, 156880, 157015
-recovered pasa_asmbl_43.p1, internal, 157356, 157479
Valid prediction for snap_scaffold_1-snap.185-T1
Valid prediction for Augustus_model.g108.t1
Valid prediction for pasa_asmbl_38.p1
Valid prediction for CodingQuarry_transcript_2516-T1
Valid prediction for GlimmerHMM_glimmerT_131-T1
Valid prediction for GlimmerHMM_glimmerT_147-T1
Valid prediction for GlimmerHMM_glimmerT_142-T1
Valid prediction for snap_scaffold_1-snap.176-T1
Valid prediction for GlimmerHMM_glimmerT_134-T1
Valid prediction for GlimmerHMM_glimmerT_130-T1
Valid prediction for Augustus_model.g118.t1
Valid prediction for CodingQuarry_transcript_2519-T1
Valid prediction for Augustus_model.g120.t1
Valid prediction for GlimmerHMM_glimmerT_151-T1
Valid prediction for snap_scaffold_1-snap.200-T1
Valid prediction for Augustus_model.g119.t1
Valid prediction for snap_scaffold_1-snap.189-T1
Valid prediction for snap_scaffold_1-snap.194-T1
Valid prediction for GlimmerHMM_glimmerT_125-T1
Valid prediction for HiQ_model.g104.t1
Valid prediction for GlimmerHMM_glimmerT_126-T1
Valid prediction for GlimmerHMM_glimmerT_137-T1
Valid prediction for HiQ_model.g106.t1
Valid prediction for snap_scaffold_1-snap.181-T1
Valid prediction for snap_scaffold_1-snap.187-T1
Valid prediction for GlimmerHMM_glimmerT_140-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17525, rend_intergenic: 11475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21543, rend_intergenic: 18211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28025, rend_intergenic: 23545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34984, rend_intergenic: 34555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85322, rend_intergenic: 84082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131551, rend_intergenic: 130169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180799, rend_intergenic: 169547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191059
-exon list size: 298


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.3    
3.7    
4.0    
4.3    
4.7    
5.0    
5.3    
5.7    
6.0    
6.3    
6.7    
7.0    
7.3    
7.7    
8.0    
8.3    
8.7    
9.0    
9.3    
9.7    
10.0    
10.3    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.7    
14.0    
14.3    
14.7    
15.0    
15.3    
15.7    
16.0    
16.3    
16.7    
17.0    
17.3    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.7    
20.0    
20.3    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.7    
23.0    
23.3    
23.7    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.3    
26.7    
27.0    
27.3    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.7    
30.0    
30.3    
30.7    
31.0    
31.3    
31.7    
32.0    
32.3    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.7    
35.0    
35.3    
35.7    
36.0    
36.3    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.7    
40.0    
40.3    
40.7    
41.0    
41.3    
41.7    
42.0    
42.3    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.7    
47.0    
47.3    
47.7    
48.0    
48.3    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.7    
52.0    
52.3    
52.7    
53.0    
53.3    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.7    
56.0    
56.3    
56.7    
57.0    
57.3    
57.7    
58.0    
58.3    
58.7    
59.0    
59.3    
59.7    
60.0    
60.3    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.7    
64.0    
64.3    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.7    
68.0    
68.3    
68.7    
69.0    
69.3    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.7    
73.0    
73.3    
73.7    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.7    
80.0    
80.3    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.7    
83.0    
83.3    
83.7    
84.0    
84.3    
84.7    
85.0    
85.3    
85.7    
86.0    
86.3    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.7    
90.0    
90.3    
90.7    
91.0    
91.3    
91.7    
92.0    
92.3    
92.7    
93.0    
93.3    
93.7    
94.0    
94.3    
94.7    
95.0    
95.3    
95.7    
96.0    
96.3    
96.7    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 17525, rend_intergenic: 11475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21543, rend_intergenic: 18211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28025, rend_intergenic: 23545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34984, rend_intergenic: 34555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85322, rend_intergenic: 84082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131551, rend_intergenic: 130169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180799, rend_intergenic: 169547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support