-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_1663669-1898480

-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 GlimmerHMM_glimmerT_8842-T1
Valid prediction for snap_scaffold_4-snap.414-T1
Valid prediction for snap_scaffold_4-snap.417-T1
Valid prediction for snap_scaffold_4-snap.422-T1
Valid prediction for snap_scaffold_4-snap.434-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8831-T1
Valid prediction for snap_scaffold_4-snap.406-T1
Valid prediction for snap_scaffold_4-snap.430-T1
Valid prediction for snap_scaffold_4-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_8835-T1
Valid prediction for GlimmerHMM_glimmerT_8837-T1
Valid prediction for Augustus_model.g5703.t1
Valid prediction for GlimmerHMM_glimmerT_8833-T1
Valid prediction for snap_scaffold_4-snap.424-T1
Valid prediction for GlimmerHMM_glimmerT_8820-T1
Valid prediction for GlimmerHMM_glimmerT_8843-T1
Couldn't classify 207783, 207976
Couldn't classify 209341, 209545
Sorry, prediction pasa_asmbl_41132.p1 fails validation.
(AGG)	 GA	207783-207976	GT	AGG
(CAA)	 AG	209341-209545	CC	TGC
Valid prediction for snap_scaffold_4-snap.397-T1
Valid prediction for snap_scaffold_4-snap.416-T1
Valid prediction for GlimmerHMM_glimmerT_8846-T1
Valid prediction for snap_scaffold_4-snap.427-T1
Valid prediction for GlimmerHMM_glimmerT_8839-T1
Valid prediction for snap_scaffold_4-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_8829-T1
Valid prediction for snap_scaffold_4-snap.436-T1
Valid prediction for snap_scaffold_4-snap.412-T1
Valid prediction for Augustus_model.g5696.t1
Valid prediction for Augustus_model.g5697.t1
Couldn't classify 213130, 213358
Couldn't classify 219866, 219916
Sorry, prediction pasa_asmbl_41133.p1 fails validation.
(AAA)	 AG	213130-213358	GT	AGG
(TTC)	 AG	214296-214340	GT	AGG
(AGT)	 AG	215949-216037	GT	AGG
(GGC)	 AG	217414-217599	GT	AGG
(TAC)	 AG	219866-219916	CC	CCC
add_exon() Sorry, pasa_asmbl_41133.p1 213130-213358-terminal-3 is invalid.
-recovered pasa_asmbl_41133.p1, terminal, 213130, 213358
-recovered pasa_asmbl_41133.p1, internal, 213130, 213358
-recovered pasa_asmbl_41133.p1, internal, 214296, 214340
-recovered pasa_asmbl_41133.p1, internal, 215949, 216037
-recovered pasa_asmbl_41133.p1, internal, 217414, 217599
Valid prediction for snap_scaffold_4-snap.399-T1
Valid prediction for snap_scaffold_4-snap.409-T1
Valid prediction for Augustus_model.g5698.t1
Valid prediction for GlimmerHMM_glimmerT_8821-T1
Valid prediction for GlimmerHMM_glimmerT_8840-T1
Couldn't classify 219992, 220259
Sorry, prediction pasa_asmbl_41135.p1 fails validation.
(CCC)	 CC	219992-220259	GT	AGG
(TGT)	 AG	221228-221271	TC	GAT
-recovered pasa_asmbl_41135.p1, terminal, 221228, 221271
Valid prediction for snap_scaffold_4-snap.440-T1
Valid prediction for Augustus_model.g5704.t1
Valid prediction for snap_scaffold_4-snap.394-T1
Valid prediction for snap_scaffold_4-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_8847-T1
Valid prediction for GlimmerHMM_glimmerT_8841-T1
Valid prediction for GlimmerHMM_glimmerT_8827-T1
Valid prediction for snap_scaffold_4-snap.401-T1
Valid prediction for Augustus_model.g5691.t1
Valid prediction for snap_scaffold_4-snap.429-T1
Valid prediction for GlimmerHMM_glimmerT_8836-T1
Valid prediction for snap_scaffold_4-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_8838-T1
Valid prediction for snap_scaffold_4-snap.403-T1
Valid prediction for Augustus_model.g5699.t1
Valid prediction for snap_scaffold_4-snap.419-T1
Valid prediction for snap_scaffold_4-snap.431-T1
Couldn't classify 226454, 226576
Couldn't classify 227315, 227455
Sorry, prediction pasa_asmbl_41136.p1 fails validation.
(GTG)	 AC	226454-226576	GT	AGG
(ATC)	 AG	226910-227017	GT	AGG
(GTC)	 AG	227315-227455	CC	TGC
-recovered pasa_asmbl_41136.p1, internal, 226910, 227017
Valid prediction for snap_scaffold_4-snap.402-T1
Valid prediction for Augustus_model.g5700.t1
Valid prediction for GlimmerHMM_glimmerT_8834-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_8830-T1
Valid prediction for snap_scaffold_4-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_8826-T1
Valid prediction for snap_scaffold_4-snap.433-T1
Valid prediction for Augustus_model.g5701.t1
Valid prediction for snap_scaffold_4-snap.411-T1
Valid prediction for snap_scaffold_4-snap.405-T1
Valid prediction for Augustus_model.g5692.t1
Valid prediction for snap_scaffold_4-snap.426-T1
Valid prediction for Augustus_model.g5689.t1
Valid prediction for GlimmerHMM_glimmerT_8823-T1
Valid prediction for snap_scaffold_4-snap.442-T1
Valid prediction for snap_scaffold_4-snap.443-T1
Valid prediction for snap_scaffold_4-snap.439-T1
Valid prediction for GlimmerHMM_glimmerT_8818-T1
Valid prediction for snap_scaffold_4-snap.432-T1
Valid prediction for snap_scaffold_4-snap.420-T1
Valid prediction for snap_scaffold_4-snap.404-T1
Valid prediction for Augustus_model.g5690.t1
Valid prediction for GlimmerHMM_glimmerT_8819-T1
Valid prediction for snap_scaffold_4-snap.441-T1
Valid prediction for snap_scaffold_4-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_8844-T1
Valid prediction for GlimmerHMM_glimmerT_8832-T1
Valid prediction for snap_scaffold_4-snap.396-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_8822-T1
Valid prediction for snap_scaffold_4-snap.410-T1
Valid prediction for snap_scaffold_4-snap.435-T1
Valid prediction for Augustus_model.g5702.t1
Valid prediction for GlimmerHMM_glimmerT_8825-T1
Valid prediction for Augustus_model.g5693.t1
Valid prediction for snap_scaffold_4-snap.444-T1
Valid prediction for Augustus_model.g5695.t1
Valid prediction for snap_scaffold_4-snap.395-T1
Valid prediction for Augustus_model.g5694.t1
Valid prediction for GlimmerHMM_glimmerT_8828-T1
Valid prediction for snap_scaffold_4-snap.438-T1
Valid prediction for GlimmerHMM_glimmerT_8824-T1
Valid prediction for snap_scaffold_4-snap.428-T1
Valid prediction for GlimmerHMM_glimmerT_8845-T1
Valid prediction for snap_scaffold_4-snap.437-T1
Valid prediction for snap_scaffold_4-snap.425-T1
Valid prediction for snap_scaffold_4-snap.415-T1
Valid prediction for snap_scaffold_4-snap.398-T1
Valid prediction for snap_scaffold_4-snap.423-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.393-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9862, rend_intergenic: 9639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13696, rend_intergenic: 10719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16802, rend_intergenic: 14659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52936, rend_intergenic: 43356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76773, rend_intergenic: 59075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79618, rend_intergenic: 77729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91307, rend_intergenic: 83337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102958, rend_intergenic: 92584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109249, rend_intergenic: 104329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132038, rend_intergenic: 127132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138122, rend_intergenic: 134100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139716, rend_intergenic: 138331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150137, rend_intergenic: 139917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153541, rend_intergenic: 151876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166966, rend_intergenic: 159201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172041, rend_intergenic: 167476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185199, rend_intergenic: 172701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227635, rend_intergenic: 201409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 137746, rend_intergenic: 137743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234812
-exon list size: 549


building trellis

0.2    
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0.9    
1.1    
1.3    
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3.8    
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25.8    
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27.8    
27.9    
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28.9    
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29.8    
29.9    
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30.9    
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31.8    
31.9    
32.1    
32.3    
32.5    
32.7    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
33.9    
34.1    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
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36.1    
36.3    
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36.7    
36.8    
37.0    
37.2    
37.4    
37.6    
37.7    
37.9    
38.1    
38.3    
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38.7    
38.8    
39.0    
39.2    
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39.6    
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39.9    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.4    
41.6    
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41.9    
42.1    
42.3    
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42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.7    
43.9    
44.1    
44.3    
44.5    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.7    
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46.8    
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47.5    
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48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.2    
49.4    
49.5    
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49.9    
50.1    
50.3    
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50.8    
51.0    
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51.4    
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52.8    
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54.1    
54.3    
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55.0    
55.2    
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56.1    
56.3    
56.4    
56.6    
56.8    
57.0    
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57.7    
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58.1    
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58.6    
58.8    
59.0    
59.2    
59.3    
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59.9    
60.1    
60.3    
60.4    
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60.8    
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61.2    
61.3    
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62.8    
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64.1    
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65.0    
65.2    
65.3    
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66.1    
66.2    
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66.6    
66.8    
67.0    
67.2    
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68.1    
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69.1    
69.3    
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71.1    
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72.1    
72.2    
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72.8    
73.0    
73.1    
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74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.7    
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80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.8    
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84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
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86.2    
86.4    
86.6    
86.8    
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87.1    
87.3    
87.5    
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87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 9862, rend_intergenic: 9639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13696, rend_intergenic: 10719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16802, rend_intergenic: 14659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52936, rend_intergenic: 43356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76773, rend_intergenic: 59075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79618, rend_intergenic: 77729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91307, rend_intergenic: 83337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102958, rend_intergenic: 92584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109249, rend_intergenic: 104329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132038, rend_intergenic: 127132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138122, rend_intergenic: 134100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139716, rend_intergenic: 138331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150137, rend_intergenic: 139917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153541, rend_intergenic: 151876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166966, rend_intergenic: 159201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172041, rend_intergenic: 167476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185199, rend_intergenic: 172701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227635, rend_intergenic: 201409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 137746, rend_intergenic: 137743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support