-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_9446261-9589669

-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_4-snap.2018-T1
Valid prediction for snap_scaffold_4-snap.2020-T1
Valid prediction for Augustus_model.g6460.t1
Valid prediction for snap_scaffold_4-snap.1998-T1
Valid prediction for GlimmerHMM_glimmerT_9940-T1
Valid prediction for snap_scaffold_4-snap.2006-T1
Valid prediction for snap_scaffold_4-snap.2001-T1
Valid prediction for Augustus_model.g6452.t1
Couldn't classify 109211, 109296
Sorry, prediction pasa_asmbl_41615.p1 fails validation.
(GCC)	 AG	109211-109296	GT	CAG
(GTT)	 AG	109610-109669	GT	GAG
(CTA)	 AG	111900-111981	GT	AGG
(GTG)	 AG	112207-112317	GT	TGG
(TCG)	 AG	113584-113688	GT	AGG
(CTG)	 AG	114699-114785	AC	AGA
-recovered pasa_asmbl_41615.p1, terminal, 114699, 114785
-recovered pasa_asmbl_41615.p1, internal, 109211, 109296
-recovered pasa_asmbl_41615.p1, internal, 109610, 109669
-recovered pasa_asmbl_41615.p1, internal, 111900, 111981
-recovered pasa_asmbl_41615.p1, internal, 112207, 112317
-recovered pasa_asmbl_41615.p1, internal, 113584, 113688
Valid prediction for snap_scaffold_4-snap.2011-T1
Valid prediction for snap_scaffold_4-snap.2022-T1
Valid prediction for snap_scaffold_4-snap.1994-T1
Valid prediction for snap_scaffold_4-snap.1995-T1
Valid prediction for Augustus_model.g6450.t1
Valid prediction for snap_scaffold_4-snap.1993-T1
Valid prediction for Augustus_model.g6453.t1
Valid prediction for Augustus_model.g6464.t1
Valid prediction for GlimmerHMM_glimmerT_9935-T1
Valid prediction for snap_scaffold_4-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_9946-T1
Valid prediction for snap_scaffold_4-snap.2013-T1
Valid prediction for GlimmerHMM_glimmerT_9933-T1
Couldn't classify 98687, 98732
Couldn't classify 104336, 104393
Sorry, prediction pasa_asmbl_41614.p1 fails validation.
(AGA)	 AA	98687-98732	GT	AGG
(AGA)	 AG	99584-99697	GT	CAG
(TCT)	 AG	101772-101836	GT	GGG
(ACC)	 AG	102679-102764	GT	AAG
(GTA)	 AG	104336-104393	GT	CGG
-recovered pasa_asmbl_41614.p1, internal, 99584, 99697
-recovered pasa_asmbl_41614.p1, internal, 101772, 101836
-recovered pasa_asmbl_41614.p1, internal, 102679, 102764
-recovered pasa_asmbl_41614.p1, internal, 104336, 104393
Valid prediction for GlimmerHMM_glimmerT_9944-T1
Valid prediction for Augustus_model.g6456.t1
Valid prediction for snap_scaffold_4-snap.2008-T1
Valid prediction for Augustus_model.g6462.t1
Valid prediction for Augustus_model.g6458.t1
Valid prediction for snap_scaffold_4-snap.2027-T1
Valid prediction for snap_scaffold_4-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_9929-T1
Valid prediction for GlimmerHMM_glimmerT_9922-T1
Valid prediction for GlimmerHMM_glimmerT_9943-T1
Valid prediction for snap_scaffold_4-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_9927-T1
Valid prediction for snap_scaffold_4-snap.2005-T1
Valid prediction for GlimmerHMM_glimmerT_9941-T1
Valid prediction for GlimmerHMM_glimmerT_9931-T1
Valid prediction for GlimmerHMM_glimmerT_9937-T1
Valid prediction for GlimmerHMM_glimmerT_9942-T1
Valid prediction for snap_scaffold_4-snap.2024-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g6459.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_9930-T1
Valid prediction for snap_scaffold_4-snap.2004-T1
Valid prediction for snap_scaffold_4-snap.1990-T1
Valid prediction for snap_scaffold_4-snap.2002-T1
Valid prediction for snap_scaffold_4-snap.2015-T1
Couldn't classify 61331, 61456
Couldn't classify 65414, 65518
Sorry, prediction pasa_asmbl_43593.p2 fails validation.
(GTG)	 AG	61331-61456	GT	ACG
(TCC)	 AG	61804-61928	GT	CAG
(GTA)	 AG	64662-64788	GT	AGG
(GAG)	 AG	65414-65518	AG	TGA
-recovered pasa_asmbl_43593.p2, internal, 61331, 61456
-recovered pasa_asmbl_43593.p2, internal, 61804, 61928
-recovered pasa_asmbl_43593.p2, internal, 64662, 64788
Valid prediction for snap_scaffold_4-snap.1991-T1
Valid prediction for Augustus_model.g6463.t1
Valid prediction for snap_scaffold_4-snap.1989-T1
Valid prediction for snap_scaffold_4-snap.1999-T1
Valid prediction for snap_scaffold_4-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_9936-T1
Valid prediction for snap_scaffold_4-snap.2019-T1
Valid prediction for snap_scaffold_4-snap.2017-T1
Valid prediction for GlimmerHMM_glimmerT_9925-T1
Valid prediction for Augustus_model.g6461.t1
Valid prediction for Augustus_model.g6454.t1
Valid prediction for GlimmerHMM_glimmerT_9928-T1
Valid prediction for snap_scaffold_4-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_9923-T1
Couldn't classify 51864, 51959
Couldn't classify 55812, 55916
Sorry, prediction pasa_asmbl_42817.p1 fails validation.
(GGC)	 CA	51864-51959	GT	AGG
(ATC)	 AG	53057-53174	GT	CTG
(CAC)	 AG	53534-53651	GT	AGG
(GGA)	 AG	55255-55297	GT	GCG
(TTC)	 AG	55812-55916	GT	TGG
-recovered pasa_asmbl_42817.p1, internal, 53057, 53174
-recovered pasa_asmbl_42817.p1, internal, 53534, 53651
-recovered pasa_asmbl_42817.p1, internal, 55255, 55297
-recovered pasa_asmbl_42817.p1, internal, 55812, 55916
Valid prediction for snap_scaffold_4-snap.2000-T1
Valid prediction for snap_scaffold_4-snap.2014-T1
Valid prediction for Augustus_model.g6446.t1
Valid prediction for snap_scaffold_4-snap.1992-T1
Valid prediction for GlimmerHMM_glimmerT_9945-T1
Valid prediction for Augustus_model.g6449.t1
Valid prediction for GlimmerHMM_glimmerT_9932-T1
Valid prediction for snap_scaffold_4-snap.2029-T1
Valid prediction for Augustus_model.g6448.t1
Valid prediction for snap_scaffold_4-snap.2007-T1
Valid prediction for snap_scaffold_4-snap.1996-T1
Valid prediction for Augustus_model.g6447.t1
Valid prediction for GlimmerHMM_glimmerT_9948-T1
Valid prediction for snap_scaffold_4-snap.2023-T1
Valid prediction for Augustus_model.g6445.t1
Valid prediction for GlimmerHMM_glimmerT_9939-T1
Valid prediction for snap_scaffold_4-snap.2026-T1
Valid prediction for GlimmerHMM_glimmerT_9926-T1
Valid prediction for GlimmerHMM_glimmerT_9924-T1
Valid prediction for GlimmerHMM_glimmerT_9938-T1
Valid prediction for snap_scaffold_4-snap.2012-T1
Valid prediction for snap_scaffold_4-snap.2025-T1
Valid prediction for snap_scaffold_4-snap.1997-T1
Valid prediction for Augustus_model.g6451.t1
Valid prediction for GlimmerHMM_glimmerT_9934-T1
Valid prediction for snap_scaffold_4-snap.2016-T1
Valid prediction for Augustus_model.g6455.t1
Valid prediction for Augustus_model.g6465.t1
Valid prediction for GlimmerHMM_glimmerT_9947-T1
Valid prediction for Augustus_model.g6457.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17218, rend_intergenic: 14548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26418, rend_intergenic: 20762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30548, rend_intergenic: 26589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33314, rend_intergenic: 30897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35476, rend_intergenic: 34568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37693, rend_intergenic: 35842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40854, rend_intergenic: 37701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41555, rend_intergenic: 41348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44345, rend_intergenic: 43980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59500, rend_intergenic: 51895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60922, rend_intergenic: 60483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68302, rend_intergenic: 66197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106803, rend_intergenic: 105915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111435, rend_intergenic: 107128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115790, rend_intergenic: 113478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120640, rend_intergenic: 117941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139200, rend_intergenic: 137387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 143409
-exon list size: 324


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 17218, rend_intergenic: 14548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26418, rend_intergenic: 20762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30548, rend_intergenic: 26589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33314, rend_intergenic: 30897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35476, rend_intergenic: 34568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37693, rend_intergenic: 35842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40854, rend_intergenic: 37701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41555, rend_intergenic: 41348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44345, rend_intergenic: 43980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59500, rend_intergenic: 51895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60922, rend_intergenic: 60483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68302, rend_intergenic: 66197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106803, rend_intergenic: 105915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111435, rend_intergenic: 107128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115790, rend_intergenic: 113478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120640, rend_intergenic: 117941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139200, rend_intergenic: 137387  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