-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_4329255-4500985

-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.g38858.t1
Valid prediction for snap_scaffold_28-snap.1051-T1
Valid prediction for snap_scaffold_28-snap.1026-T1
Valid prediction for snap_scaffold_28-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_58667-T1
Valid prediction for GlimmerHMM_glimmerT_58662-T1
Valid prediction for Augustus_model.g38851.t1
Valid prediction for GlimmerHMM_glimmerT_58661-T1
Valid prediction for snap_scaffold_28-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_58655-T1
Valid prediction for snap_scaffold_28-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_58665-T1
Valid prediction for snap_scaffold_28-snap.1033-T1
Valid prediction for GlimmerHMM_glimmerT_58663-T1
Valid prediction for GlimmerHMM_glimmerT_58670-T1
Valid prediction for Augustus_model.g38862.t1
Valid prediction for GlimmerHMM_glimmerT_58644-T1
Valid prediction for GlimmerHMM_glimmerT_58648-T1
Valid prediction for GlimmerHMM_glimmerT_58664-T1
Valid prediction for GlimmerHMM_glimmerT_58646-T1
Valid prediction for GlimmerHMM_glimmerT_58657-T1
Valid prediction for GlimmerHMM_glimmerT_58651-T1
Valid prediction for snap_scaffold_28-snap.1035-T1
Valid prediction for snap_scaffold_28-snap.1043-T1
Couldn't classify 125751, 125797
Sorry, prediction pasa_asmbl_37534.p1 fails validation.
(AGG)	 GC	125751-125797	GT	AAG
(GTG)	 AG	126589-126807	GT	AGG
(TTG)	 AG	127130-127258	GT	TAG
(CTG)	 AG	127402-127505	GT	ACG
(AGC)	 AG	128852-128966	GT	AAG
(TCC)	 AG	129244-129368	GT	TGG
(TAG)	 AG	132111-132260	GT	AGG
(AGT)	 AG	132643-133856	TT	GAT
-recovered pasa_asmbl_37534.p1, terminal, 132643, 133856
-recovered pasa_asmbl_37534.p1, internal, 126589, 126807
-recovered pasa_asmbl_37534.p1, internal, 127130, 127258
-recovered pasa_asmbl_37534.p1, internal, 127402, 127505
-recovered pasa_asmbl_37534.p1, internal, 128852, 128966
-recovered pasa_asmbl_37534.p1, internal, 129244, 129368
-recovered pasa_asmbl_37534.p1, internal, 132111, 132260
Valid prediction for GlimmerHMM_glimmerT_58660-T1
Valid prediction for GlimmerHMM_glimmerT_58668-T1
Valid prediction for snap_scaffold_28-snap.1034-T1
Valid prediction for snap_scaffold_28-snap.1046-T1
Valid prediction for GlimmerHMM_glimmerT_58643-T1
Valid prediction for snap_scaffold_28-snap.1027-T1
Valid prediction for snap_scaffold_28-snap.1048-T1
Valid prediction for snap_scaffold_28-snap.1032-T1
Valid prediction for snap_scaffold_28-snap.1039-T1
Valid prediction for Augustus_model.g38860.t1
Valid prediction for Augustus_model.g38853.t1
Valid prediction for GlimmerHMM_glimmerT_58656-T1
Valid prediction for GlimmerHMM_glimmerT_58654-T1
Valid prediction for Augustus_model.g38863.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_28-snap.1022-T1
Valid prediction for snap_scaffold_28-snap.1054-T1
Valid prediction for snap_scaffold_28-snap.1049-T1
Valid prediction for snap_scaffold_28-snap.1050-T1
Valid prediction for snap_scaffold_28-snap.1044-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g38854.t1
Valid prediction for GlimmerHMM_glimmerT_58653-T1
Valid prediction for Augustus_model.g38856.t1
Valid prediction for GlimmerHMM_glimmerT_58659-T1
Valid prediction for snap_scaffold_28-snap.1053-T1
Valid prediction for snap_scaffold_28-snap.1045-T1
Valid prediction for CodingQuarry_transcript_43636-T1
Valid prediction for snap_scaffold_28-snap.1047-T1
Couldn't classify 120696, 121616
Sorry, prediction pasa_asmbl_38207.p1 fails validation.
(CTG)	 AC	120696-121616	GA	AGG
Valid prediction for Augustus_model.g38861.t1
Valid prediction for GlimmerHMM_glimmerT_58647-T1
Valid prediction for GlimmerHMM_glimmerT_58666-T1
Valid prediction for GlimmerHMM_glimmerT_58645-T1
Valid prediction for snap_scaffold_28-snap.1041-T1
Valid prediction for Augustus_model.g38865.t1
Valid prediction for Augustus_model.g38852.t1
Valid prediction for snap_scaffold_28-snap.1036-T1
Valid prediction for Augustus_model.g38855.t1
Valid prediction for snap_scaffold_28-snap.1029-T1
Valid prediction for snap_scaffold_28-snap.1038-T1
Valid prediction for snap_scaffold_28-snap.1052-T1
Valid prediction for snap_scaffold_28-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_58650-T1
Valid prediction for snap_scaffold_28-snap.1040-T1
Valid prediction for pasa_asmbl_38208.p1
Valid prediction for GlimmerHMM_glimmerT_58649-T1
Valid prediction for snap_scaffold_28-snap.1028-T1
Valid prediction for GlimmerHMM_glimmerT_58658-T1
Valid prediction for snap_scaffold_28-snap.1025-T1
Valid prediction for Augustus_model.g38864.t1
Valid prediction for GlimmerHMM_glimmerT_58669-T1
Valid prediction for snap_scaffold_28-snap.1042-T1
Valid prediction for GlimmerHMM_glimmerT_58652-T1
Valid prediction for snap_scaffold_28-snap.1031-T1
Valid prediction for HiQ_model.g38859.t1
Valid prediction for Augustus_model.g38857.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 104344, rend_intergenic: 103548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107704, rend_intergenic: 104729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133856, rend_intergenic: 124053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144994, rend_intergenic: 143549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171731
-exon list size: 235


building trellis

0.4    
0.8    
1.3    
1.7    
2.1    
2.5    
3.0    
3.4    
3.8    
4.2    
4.6    
5.1    
5.5    
5.9    
6.3    
6.8    
7.2    
7.6    
8.0    
8.4    
8.9    
9.3    
9.7    
10.1    
10.5    
11.0    
11.4    
11.8    
12.2    
12.7    
13.1    
13.5    
13.9    
14.3    
14.8    
15.2    
15.6    
16.0    
16.5    
16.9    
17.3    
17.7    
18.1    
18.6    
19.0    
19.4    
19.8    
20.3    
20.7    
21.1    
21.5    
21.9    
22.4    
22.8    
23.2    
23.6    
24.1    
24.5    
24.9    
25.3    
25.7    
26.2    
26.6    
27.0    
27.4    
27.8    
28.3    
28.7    
29.1    
29.5    
30.0    
30.4    
30.8    
31.2    
31.6    
32.1    
32.5    
32.9    
33.3    
33.8    
34.2    
34.6    
35.0    
35.4    
35.9    
36.3    
36.7    
37.1    
37.6    
38.0    
38.4    
38.8    
39.2    
39.7    
40.1    
40.5    
40.9    
41.4    
41.8    
42.2    
42.6    
43.0    
43.5    
43.9    
44.3    
44.7    
45.1    
45.6    
46.0    
46.4    
46.8    
47.3    
47.7    
48.1    
48.5    
48.9    
49.4    
49.8    
50.2    
50.6    
51.1    
51.5    
51.9    
52.3    
52.7    
53.2    
53.6    
54.0    
54.4    
54.9    
55.3    
55.7    
56.1    
56.5    
57.0    
57.4    
57.8    
58.2    
58.6    
59.1    
59.5    
59.9    
60.3    
60.8    
61.2    
61.6    
62.0    
62.4    
62.9    
63.3    
63.7    
64.1    
64.6    
65.0    
65.4    
65.8    
66.2    
66.7    
67.1    
67.5    
67.9    
68.4    
68.8    
69.2    
69.6    
70.0    
70.5    
70.9    
71.3    
71.7    
72.2    
72.6    
73.0    
73.4    
73.8    
74.3    
74.7    
75.1    
75.5    
75.9    
76.4    
76.8    
77.2    
77.6    
78.1    
78.5    
78.9    
79.3    
79.7    
80.2    
80.6    
81.0    
81.4    
81.9    
82.3    
82.7    
83.1    
83.5    
84.0    
84.4    
84.8    
85.2    
85.7    
86.1    
86.5    
86.9    
87.3    
87.8    
88.2    
88.6    
89.0    
89.5    
89.9    
90.3    
90.7    
91.1    
91.6    
92.0    
92.4    
92.8    
93.2    
93.7    
94.1    
94.5    
94.9    
95.4    
95.8    
96.2    
96.6    
97.0    
97.5    
97.9    
98.3    
98.7    
99.2    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 104344, rend_intergenic: 103548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107704, rend_intergenic: 104729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133856, rend_intergenic: 124053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144994, rend_intergenic: 143549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support