-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_12731601-12926431

-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 GeneMark_model.7756_t
Valid prediction for GeneMark_model.7716_t
Valid prediction for GeneMark_model.7745_t
Valid prediction for GeneMark_model.7710_t
Valid prediction for Augustus_model.g3226.t1
Valid prediction for snap_scaffold_2-snap.2474-T1
Valid prediction for GeneMark_model.7732_t
Valid prediction for GeneMark_model.7729_t
Valid prediction for GeneMark_model.7753_t
Valid prediction for GeneMark_model.7708_t
Valid prediction for GlimmerHMM_glimmerT_4824-T1
Valid prediction for GeneMark_model.7704_t
Valid prediction for Augustus_model.g3240.t1
Valid prediction for GeneMark_model.7731_t
Valid prediction for snap_scaffold_2-snap.2503-T1
Valid prediction for snap_scaffold_2-snap.2473-T1
Valid prediction for GeneMark_model.7736_t
Valid prediction for GeneMark_model.7760_t
Valid prediction for Augustus_model.g3235.t1
Valid prediction for GlimmerHMM_glimmerT_4817-T1
Valid prediction for Augustus_model.g3233.t1
Valid prediction for GeneMark_model.7739_t
Valid prediction for Augustus_model.g3239.t1
Valid prediction for GeneMark_model.7740_t
Valid prediction for GeneMark_model.7751_t
Valid prediction for Augustus_model.g3241.t1
Valid prediction for Augustus_model.g3228.t1
Valid prediction for snap_scaffold_2-snap.2492-T1
Valid prediction for snap_scaffold_2-snap.2496-T1
Valid prediction for snap_scaffold_2-snap.2508-T1
Valid prediction for GeneMark_model.7714_t
Valid prediction for GlimmerHMM_glimmerT_4825-T1
Valid prediction for GlimmerHMM_glimmerT_4830-T1
Valid prediction for snap_scaffold_2-snap.2486-T1
Valid prediction for GeneMark_model.7743_t
Valid prediction for GlimmerHMM_glimmerT_4818-T1
Valid prediction for GlimmerHMM_glimmerT_4827-T1
Valid prediction for GeneMark_model.7758_t
Valid prediction for GlimmerHMM_glimmerT_4801-T1
Valid prediction for GeneMark_model.7734_t
Valid prediction for GeneMark_model.7771_t
Valid prediction for Augustus_model.g3238.t1
Valid prediction for snap_scaffold_2-snap.2479-T1
Valid prediction for GeneMark_model.7738_t
Valid prediction for GeneMark_model.7726_t
Valid prediction for snap_scaffold_2-snap.2504-T1
Valid prediction for GeneMark_model.7769_t
Valid prediction for GlimmerHMM_glimmerT_4815-T1
Valid prediction for GeneMark_model.7764_t
Valid prediction for Augustus_model.g3234.t1
Valid prediction for snap_scaffold_2-snap.2489-T1
Valid prediction for GeneMark_model.7747_t
Valid prediction for GeneMark_model.7723_t
Valid prediction for snap_scaffold_2-snap.2498-T1
Valid prediction for GeneMark_model.7755_t
Valid prediction for snap_scaffold_2-snap.2493-T1
Valid prediction for GeneMark_model.7718_t
Valid prediction for snap_scaffold_2-snap.2470-T1
Valid prediction for GeneMark_model.7703_t
Valid prediction for snap_scaffold_2-snap.2478-T1
Valid prediction for GlimmerHMM_glimmerT_4828-T1
Valid prediction for GlimmerHMM_glimmerT_4819-T1
Valid prediction for GeneMark_model.7741_t
Valid prediction for GeneMark_model.7762_t
Valid prediction for GeneMark_model.7721_t
Valid prediction for snap_scaffold_2-snap.2477-T1
Valid prediction for snap_scaffold_2-snap.2506-T1
Valid prediction for snap_scaffold_2-snap.2466-T1
Valid prediction for snap_scaffold_2-snap.2481-T1
Valid prediction for GlimmerHMM_glimmerT_4823-T1
Valid prediction for GeneMark_model.7719_t
Valid prediction for GlimmerHMM_glimmerT_4822-T1
Valid prediction for snap_scaffold_2-snap.2469-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_4810-T1
Valid prediction for Augustus_model.g3230.t1
Valid prediction for GeneMark_model.7746_t
Valid prediction for GlimmerHMM_glimmerT_4820-T1
Valid prediction for snap_scaffold_2-snap.2499-T1
Valid prediction for GeneMark_model.7761_t
Valid prediction for GeneMark_model.7724_t
Valid prediction for GeneMark_model.7711_t
Valid prediction for GlimmerHMM_glimmerT_4814-T1
Valid prediction for GlimmerHMM_glimmerT_4826-T1
Valid prediction for snap_scaffold_2-snap.2490-T1
Valid prediction for GeneMark_model.7725_t
Valid prediction for Augustus_model.g3243.t1
Valid prediction for snap_scaffold_2-snap.2497-T1
Valid prediction for Augustus_model.g3232.t1
Valid prediction for snap_scaffold_2-snap.2509-T1
Valid prediction for GeneMark_model.7728_t
Valid prediction for GlimmerHMM_glimmerT_4800-T1
Valid prediction for GeneMark_model.7717_t
Valid prediction for GeneMark_model.7759_t
Valid prediction for snap_scaffold_2-snap.2505-T1
Valid prediction for GeneMark_model.7707_t
Valid prediction for Augustus_model.g3244.t1
Valid prediction for GlimmerHMM_glimmerT_4831-T1
Valid prediction for snap_scaffold_2-snap.2472-T1
Valid prediction for GeneMark_model.7727_t
Valid prediction for GlimmerHMM_glimmerT_4816-T1
Valid prediction for GeneMark_model.7766_t
Valid prediction for GeneMark_model.7720_t
Valid prediction for GeneMark_model.7772_t
Couldn't classify 38075, 38150
Sorry, prediction pasa_asmbl_23496.p1 fails validation.
(ATT)	 CC	38075-38150	GT	GGG
(ACC)	 AG	38302-38404	GT	AGG
(GTT)	 AG	38623-38704	GT	AGG
(ATG)	 AG	39357-39425	GT	AGG
(CTG)	 AG	39578-39691	GT	AGG
(GCC)	 AG	39899-40114	GG	GAG
-recovered pasa_asmbl_23496.p1, initial, 39357, 39425
-recovered pasa_asmbl_23496.p1, terminal, 39899, 40114
-recovered pasa_asmbl_23496.p1, internal, 38302, 38404
-recovered pasa_asmbl_23496.p1, internal, 38623, 38704
-recovered pasa_asmbl_23496.p1, internal, 39357, 39425
-recovered pasa_asmbl_23496.p1, internal, 39578, 39691
Valid prediction for GeneMark_model.7742_t
Valid prediction for GlimmerHMM_glimmerT_4829-T1
Valid prediction for snap_scaffold_2-snap.2484-T1
Valid prediction for GeneMark_model.7712_t
Valid prediction for snap_scaffold_2-snap.2485-T1
Valid prediction for GeneMark_model.7744_t
Valid prediction for GlimmerHMM_glimmerT_4812-T1
Valid prediction for GeneMark_model.7770_t
Valid prediction for GlimmerHMM_glimmerT_4811-T1
Valid prediction for GeneMark_model.7705_t
Valid prediction for GeneMark_model.7754_t
Valid prediction for GlimmerHMM_glimmerT_4806-T1
Valid prediction for snap_scaffold_2-snap.2501-T1
Valid prediction for GeneMark_model.7768_t
Valid prediction for snap_scaffold_2-snap.2487-T1
Valid prediction for GlimmerHMM_glimmerT_4802-T1
Valid prediction for GlimmerHMM_glimmerT_4813-T1
Valid prediction for Augustus_model.g3237.t1
Valid prediction for GlimmerHMM_glimmerT_4803-T1
Valid prediction for GlimmerHMM_glimmerT_4809-T1
Valid prediction for Augustus_model.g3227.t1
Valid prediction for snap_scaffold_2-snap.2467-T1
Valid prediction for GeneMark_model.7735_t
Valid prediction for GeneMark_model.7715_t
Valid prediction for GeneMark_model.7763_t
Valid prediction for snap_scaffold_2-snap.2491-T1
Valid prediction for snap_scaffold_2-snap.2468-T1
Valid prediction for GeneMark_model.7733_t
Valid prediction for GeneMark_model.7713_t
Valid prediction for GlimmerHMM_glimmerT_4804-T1
Valid prediction for GeneMark_model.7706_t
Valid prediction for snap_scaffold_2-snap.2494-T1
Valid prediction for Augustus_model.g3231.t1
Valid prediction for GlimmerHMM_glimmerT_4808-T1
Valid prediction for snap_scaffold_2-snap.2500-T1
Valid prediction for snap_scaffold_2-snap.2507-T1
Valid prediction for snap_scaffold_2-snap.2480-T1
Valid prediction for GlimmerHMM_glimmerT_4805-T1
Valid prediction for snap_scaffold_2-snap.2483-T1
Valid prediction for snap_scaffold_2-snap.2475-T1
Valid prediction for GeneMark_model.7737_t
Valid prediction for GeneMark_model.7752_t
Valid prediction for GeneMark_model.7701_t
Valid prediction for GeneMark_model.7702_t
Valid prediction for snap_scaffold_2-snap.2495-T1
Valid prediction for snap_scaffold_2-snap.2502-T1
Valid prediction for GeneMark_model.7749_t
Valid prediction for GeneMark_model.7767_t
Valid prediction for GlimmerHMM_glimmerT_4807-T1
Valid prediction for snap_scaffold_2-snap.2482-T1
Valid prediction for GlimmerHMM_glimmerT_4821-T1
Valid prediction for GeneMark_model.7757_t
Valid prediction for snap_scaffold_2-snap.2488-T1
Valid prediction for GeneMark_model.7748_t
Valid prediction for snap_scaffold_2-snap.2471-T1
Valid prediction for GeneMark_model.7722_t
Valid prediction for GeneMark_model.7765_t
Valid prediction for GeneMark_model.7750_t
Valid prediction for Augustus_model.g3236.t1
Valid prediction for GeneMark_model.7709_t
Valid prediction for GeneMark_model.7730_t
Valid prediction for Augustus_model.g3229.t1
Valid prediction for Augustus_model.g3242.t1
Valid prediction for snap_scaffold_2-snap.2476-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13633, rend_intergenic: 5710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23798, rend_intergenic: 15151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39964, rend_intergenic: 28292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47293, rend_intergenic: 42695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60389, rend_intergenic: 48403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76248, rend_intergenic: 60658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88576, rend_intergenic: 79662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92450, rend_intergenic: 88772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96821, rend_intergenic: 92950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105315, rend_intergenic: 103744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111976, rend_intergenic: 105358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124393, rend_intergenic: 117291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125950, rend_intergenic: 124461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132673, rend_intergenic: 127895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149498, rend_intergenic: 133054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160527, rend_intergenic: 156095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168676, rend_intergenic: 160553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169432, rend_intergenic: 169252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188595, rend_intergenic: 172393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190914, rend_intergenic: 188746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194831
-exon list size: 941


building trellis

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66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 13633, rend_intergenic: 5710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23798, rend_intergenic: 15151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39964, rend_intergenic: 28292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47293, rend_intergenic: 42695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60389, rend_intergenic: 48403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76248, rend_intergenic: 60658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88576, rend_intergenic: 79662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92450, rend_intergenic: 88772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96821, rend_intergenic: 92950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105315, rend_intergenic: 103744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111976, rend_intergenic: 105358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124393, rend_intergenic: 117291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125950, rend_intergenic: 124461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132673, rend_intergenic: 127895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149498, rend_intergenic: 133054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160527, rend_intergenic: 156095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168676, rend_intergenic: 160553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169432, rend_intergenic: 169252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188595, rend_intergenic: 172393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190914, rend_intergenic: 188746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12717
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support