-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_16861693-16991766

-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.g3680.t1
Valid prediction for GeneMark_model.8736_t
Valid prediction for GlimmerHMM_glimmerT_5443-T1
Valid prediction for GeneMark_model.8713_t
Valid prediction for GeneMark_model.8738_t
Valid prediction for snap_scaffold_2-snap.3284-T1
Valid prediction for snap_scaffold_2-snap.3308-T1
Valid prediction for GlimmerHMM_glimmerT_5441-T1
Valid prediction for GeneMark_model.8748_t
Valid prediction for snap_scaffold_2-snap.3316-T1
Valid prediction for snap_scaffold_2-snap.3287-T1
Valid prediction for GlimmerHMM_glimmerT_5440-T1
Valid prediction for snap_scaffold_2-snap.3282-T1
Valid prediction for GeneMark_model.8719_t
Valid prediction for snap_scaffold_2-snap.3288-T1
Valid prediction for GlimmerHMM_glimmerT_5436-T1
Valid prediction for snap_scaffold_2-snap.3313-T1
Valid prediction for snap_scaffold_2-snap.3292-T1
Valid prediction for snap_scaffold_2-snap.3290-T1
Valid prediction for snap_scaffold_2-snap.3309-T1
Valid prediction for snap_scaffold_2-snap.3280-T1
Valid prediction for GlimmerHMM_glimmerT_5428-T1
Valid prediction for GlimmerHMM_glimmerT_5442-T1
Valid prediction for Augustus_model.g3672.t1
Valid prediction for Augustus_model.g3674.t1
Valid prediction for Augustus_model.g3679.t1
Valid prediction for GeneMark_model.8718_t
Valid prediction for snap_scaffold_2-snap.3315-T1
Valid prediction for GeneMark_model.8752_t
Valid prediction for GeneMark_model.8708_t
Valid prediction for snap_scaffold_2-snap.3295-T1
Valid prediction for GeneMark_model.8742_t
Valid prediction for GeneMark_model.8710_t
Valid prediction for Augustus_model.g3682.t1
Valid prediction for GlimmerHMM_glimmerT_5432-T1
Valid prediction for snap_scaffold_2-snap.3300-T1
Valid prediction for GeneMark_model.8727_t
Valid prediction for GeneMark_model.8750_t
Valid prediction for snap_scaffold_2-snap.3305-T1
Valid prediction for snap_scaffold_2-snap.3311-T1
Valid prediction for Augustus_model.g3683.t1
Valid prediction for GeneMark_model.8745_t
Valid prediction for GeneMark_model.8723_t
Couldn't classify 5974, 6038
Sorry, prediction pasa_asmbl_25187.p1 fails validation.
(ATG)	 TG	2636-2788	GT	GGG
(GTG)	 AG	3359-3466	GT	AGG
(TGT)	 AG	4091-4277	GT	ACG
(TCT)	 AG	5974-6038	CA	GCC
-recovered pasa_asmbl_25187.p1, initial, 2636, 2788
-recovered pasa_asmbl_25187.p1, internal, 3359, 3466
-recovered pasa_asmbl_25187.p1, internal, 4091, 4277
Valid prediction for GeneMark_model.8715_t
Valid prediction for GlimmerHMM_glimmerT_5434-T1
Valid prediction for Augustus_model.g3678.t1
Valid prediction for Augustus_model.g3681.t1
Valid prediction for GeneMark_model.8729_t
Valid prediction for GlimmerHMM_glimmerT_5445-T1
Valid prediction for GeneMark_model.8747_t
Valid prediction for GlimmerHMM_glimmerT_5429-T1
Valid prediction for snap_scaffold_2-snap.3304-T1
Valid prediction for GeneMark_model.8721_t
Valid prediction for GlimmerHMM_glimmerT_5444-T1
Valid prediction for GeneMark_model.8740_t

-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 GeneMark_model.8725_t
Valid prediction for snap_scaffold_2-snap.3306-T1
Valid prediction for Augustus_model.g3675.t1
Valid prediction for snap_scaffold_2-snap.3286-T1
Valid prediction for GeneMark_model.8735_t
Valid prediction for GeneMark_model.8734_t
Valid prediction for GeneMark_model.8714_t
Valid prediction for GeneMark_model.8751_t
Valid prediction for GeneMark_model.8722_t
Valid prediction for snap_scaffold_2-snap.3293-T1
Valid prediction for GeneMark_model.8732_t
Valid prediction for snap_scaffold_2-snap.3294-T1
Valid prediction for snap_scaffold_2-snap.3281-T1
Valid prediction for GeneMark_model.8743_t
Valid prediction for snap_scaffold_2-snap.3283-T1
Valid prediction for snap_scaffold_2-snap.3314-T1
Valid prediction for GeneMark_model.8737_t
Valid prediction for GeneMark_model.8720_t
Valid prediction for GeneMark_model.8728_t
Valid prediction for snap_scaffold_2-snap.3299-T1
Valid prediction for Augustus_model.g3676.t1
Valid prediction for GlimmerHMM_glimmerT_5435-T1
Valid prediction for snap_scaffold_2-snap.3297-T1
Valid prediction for snap_scaffold_2-snap.3291-T1
Valid prediction for GeneMark_model.8726_t
Valid prediction for GeneMark_model.8716_t
Valid prediction for GlimmerHMM_glimmerT_5433-T1
Valid prediction for Augustus_model.g3677.t1
Valid prediction for GeneMark_model.8744_t
Valid prediction for GeneMark_model.8731_t
Valid prediction for snap_scaffold_2-snap.3302-T1
Valid prediction for GeneMark_model.8730_t
Valid prediction for GeneMark_model.8717_t
Valid prediction for snap_scaffold_2-snap.3289-T1
Valid prediction for GlimmerHMM_glimmerT_5437-T1
Valid prediction for GeneMark_model.8711_t
Valid prediction for GeneMark_model.8707_t
Valid prediction for GeneMark_model.8733_t
Valid prediction for snap_scaffold_2-snap.3312-T1
Valid prediction for GeneMark_model.8709_t
Valid prediction for snap_scaffold_2-snap.3307-T1
Valid prediction for snap_scaffold_2-snap.3303-T1
Valid prediction for GlimmerHMM_glimmerT_5438-T1
Valid prediction for Augustus_model.g3673.t1
Valid prediction for GlimmerHMM_glimmerT_5439-T1
Valid prediction for GeneMark_model.8746_t
Valid prediction for GeneMark_model.8749_t
Valid prediction for snap_scaffold_2-snap.3296-T1
Valid prediction for snap_scaffold_2-snap.3285-T1
Valid prediction for snap_scaffold_2-snap.3301-T1
Valid prediction for GeneMark_model.8724_t
Valid prediction for GlimmerHMM_glimmerT_5431-T1
Valid prediction for GeneMark_model.8712_t
Valid prediction for snap_scaffold_2-snap.3310-T1
Valid prediction for snap_scaffold_2-snap.3298-T1
Valid prediction for GlimmerHMM_glimmerT_5430-T1
Valid prediction for GeneMark_model.8739_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4464, rend_intergenic: 2446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5876, rend_intergenic: 5082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8502, rend_intergenic: 5943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19082, rend_intergenic: 16526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21576, rend_intergenic: 20054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27960, rend_intergenic: 24072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37296, rend_intergenic: 29530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38602, rend_intergenic: 38039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42098, rend_intergenic: 40555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64963, rend_intergenic: 64669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77384, rend_intergenic: 65228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101506, rend_intergenic: 97155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109460, rend_intergenic: 103284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115386, rend_intergenic: 110506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122132, rend_intergenic: 118355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 130074
-exon list size: 551


building trellis

0.2    
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3.8    
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17.0    
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19.3    
19.5    
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20.1    
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20.8    
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21.2    
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23.0    
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24.8    
25.0    
25.1    
25.3    
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27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
28.9    
29.1    
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30.2    
30.4    
30.6    
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30.9    
31.1    
31.3    
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31.6    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
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34.5    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
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36.9    
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37.8    
38.0    
38.2    
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38.9    
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40.7    
40.9    
41.0    
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44.7    
44.8    
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57.0    
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58.8    
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59.9    
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61.3    
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64.2    
64.4    
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65.1    
65.3    
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66.0    
66.2    
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66.9    
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67.6    
67.8    
68.0    
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68.9    
69.1    
69.3    
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69.6    
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71.1    
71.2    
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71.8    
72.0    
72.2    
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72.9    
73.1    
73.2    
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73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
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74.9    
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75.2    
75.4    
75.6    
75.8    
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76.1    
76.3    
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76.9    
77.0    
77.2    
77.4    
77.6    
77.8    
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78.1    
78.3    
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78.7    
78.8    
79.0    
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79.4    
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80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.7    
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    
98.6    
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: 4464, rend_intergenic: 2446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5876, rend_intergenic: 5082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8502, rend_intergenic: 5943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19082, rend_intergenic: 16526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21576, rend_intergenic: 20054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27960, rend_intergenic: 24072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37296, rend_intergenic: 29530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38602, rend_intergenic: 38039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42098, rend_intergenic: 40555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64963, rend_intergenic: 64669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77384, rend_intergenic: 65228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101506, rend_intergenic: 97155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109460, rend_intergenic: 103284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115386, rend_intergenic: 110506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122132, rend_intergenic: 118355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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